gromacs →
2020.3-1 →
armhf → 2020-07-16 01:18:26
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on testbuildd
+==============================================================================+
| gromacs 2020.3-1 (armhf) Wed, 15 Jul 2020 12:42:24 +0000 |
+==============================================================================+
Package: gromacs
Version: 2020.3-1
Source Version: 2020.3-1
Distribution: bullseye-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bullseye-staging-armhf-sbuild-ed0524e9-90c0-451f-87b1-c0a5cca4714b' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bullseye-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bullseye-staging/main Sources [11.7 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [12.8 MB]
Fetched 24.6 MB in 27s (919 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'gromacs' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/debichem-team/gromacs.git
Please use:
git clone https://salsa.debian.org/debichem-team/gromacs.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 29.2 MB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main gromacs 2020.3-1 (dsc) [2581 B]
Get:2 http://172.17.0.1/private bullseye-staging/main gromacs 2020.3-1 (tar) [29.1 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main gromacs 2020.3-1 (diff) [37.2 kB]
Fetched 29.2 MB in 9s (3318 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/gromacs-uoIy6w/gromacs-2020.3' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/gromacs-uoIy6w' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install build-essential |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-vm1oud/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-vm1oud/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-vm1oud/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-vm1oud/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-vm1oud/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-vm1oud/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-vm1oud/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-vm1oud/apt_archive ./ Packages [433 B]
Fetched 2109 B in 1s (2684 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
bsdextrautils netbase
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 3 not upgraded.
Need to get 848 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-vm1oud/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [848 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 848 B in 0s (22.8 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12289 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any all)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: chrpath, cmake, debhelper (>= 12), libblas-dev, libboost-dev, libfftw3-dev, liblapack-dev, libmpich-dev (>= 3.0.4-6), libopenmpi-dev (>= 1.10.2-7), libx11-dev, lsb-release, mpich, openmpi-bin, zlib1g-dev
Filtered Build-Depends: chrpath, cmake, debhelper (>= 12), libblas-dev, libboost-dev, libfftw3-dev, liblapack-dev, libmpich-dev (>= 3.0.4-6), libopenmpi-dev (>= 1.10.2-7), libx11-dev, lsb-release, mpich, openmpi-bin, zlib1g-dev
dpkg-deb: building package 'sbuild-build-depends-gromacs-dummy' in '/<<BUILDDIR>>/resolver-vm1oud/apt_archive/sbuild-build-depends-gromacs-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-gromacs-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-vm1oud/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-vm1oud/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-vm1oud/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-vm1oud/apt_archive ./ Sources [584 B]
Get:5 copy:/<<BUILDDIR>>/resolver-vm1oud/apt_archive ./ Packages [661 B]
Fetched 2578 B in 1s (3463 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install gromacs build dependencies (apt-based resolver)
-------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following package was automatically installed and is no longer required:
netbase
Use 'apt autoremove' to remove it.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev chrpath cmake cmake-data debhelper
dh-autoreconf dh-strip-nondeterminism distro-info-data dwz file gettext
gettext-base gfortran gfortran-9 groff-base hwloc-nox ibverbs-providers
intltool-debian libarchive-zip-perl libarchive13 libblas-dev libblas3
libboost-dev libboost1.71-dev libbrotli1 libbsd0 libcbor0 libcroco3 libcurl4
libdebhelper-perl libedit2 libelf1 libevent-2.1-7 libevent-core-2.1-7
libevent-dev libevent-extra-2.1-7 libevent-openssl-2.1-7
libevent-pthreads-2.1-7 libexpat1 libfftw3-bin libfftw3-dev libfftw3-double3
libfftw3-single3 libfido2-1 libfile-stripnondeterminism-perl
libgfortran-9-dev libgfortran5 libglib2.0-0 libgssapi-krb5-2 libhwloc-dev
libhwloc-plugins libhwloc15 libibverbs-dev libibverbs1 libicu67 libjsoncpp1
libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack-dev liblapack3
libltdl-dev libltdl7 libmagic-mgc libmagic1 libmpdec2 libmpich-dev
libmpich12 libncurses6 libnghttp2-14 libnl-3-200 libnl-3-dev
libnl-route-3-200 libnl-route-3-dev libnuma-dev libnuma1 libopenmpi-dev
libopenmpi3 libpciaccess0 libpipeline1 libpmix2 libprocps8 libpsl5
libpthread-stubs0-dev libpython3-stdlib libpython3.8-minimal
libpython3.8-stdlib librhash0 librtmp1 libsigsegv2 libssh2-1
libsub-override-perl libtool libuchardet0 libuv1 libx11-6 libx11-data
libx11-dev libxau-dev libxau6 libxcb1 libxcb1-dev libxdmcp-dev libxdmcp6
libxext6 libxml2 libxnvctrl0 lsb-release m4 man-db mime-support mpich
ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client po-debconf
procps python3 python3-minimal python3.8 python3.8-minimal sensible-utils
x11proto-core-dev x11proto-dev xorg-sgml-doctools xtrans-dev zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc cmake-doc ninja-build dh-make
gettext-doc libasprintf-dev libgettextpo-dev gfortran-doc gfortran-9-doc
libcoarrays-dev groff lrzip liblapack-doc libboost-doc libboost1.71-doc
libboost-atomic1.71-dev libboost-chrono1.71-dev libboost-container1.71-dev
libboost-context1.71-dev libboost-contract1.71-dev
libboost-coroutine1.71-dev libboost-date-time1.71-dev
libboost-exception1.71-dev libboost-fiber1.71-dev
libboost-filesystem1.71-dev libboost-graph1.71-dev
libboost-graph-parallel1.71-dev libboost-iostreams1.71-dev
libboost-locale1.71-dev libboost-log1.71-dev libboost-math1.71-dev
libboost-mpi1.71-dev libboost-mpi-python1.71-dev libboost-numpy1.71-dev
libboost-program-options1.71-dev libboost-python1.71-dev
libboost-random1.71-dev libboost-regex1.71-dev
libboost-serialization1.71-dev libboost-stacktrace1.71-dev
libboost-system1.71-dev libboost-test1.71-dev libboost-thread1.71-dev
libboost-timer1.71-dev libboost-type-erasure1.71-dev libboost-wave1.71-dev
libboost1.71-tools-dev libmpfrc++-dev libntl-dev libfftw3-doc krb5-doc
krb5-user libtool-doc openmpi-doc pciutils gcj-jdk libx11-doc libxcb-doc
m4-doc apparmor less www-browser mpich-doc opencl-icd keychain libpam-ssh
monkeysphere ssh-askpass libmail-box-perl python3-doc python3-tk
python3-venv python3.8-venv python3.8-doc binfmt-support
Recommended packages:
curl | wget | lynx ca-certificates libarchive-cpio-perl libglib2.0-data
shared-mime-info xdg-user-dirs krb5-locales libgpm2 libcoarrays-openmpi-dev
publicsuffix xauth libmail-sendmail-perl psmisc
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev chrpath cmake cmake-data debhelper
dh-autoreconf dh-strip-nondeterminism distro-info-data dwz file gettext
gettext-base gfortran gfortran-9 groff-base hwloc-nox ibverbs-providers
intltool-debian libarchive-zip-perl libarchive13 libblas-dev libblas3
libboost-dev libboost1.71-dev libbrotli1 libbsd0 libcbor0 libcroco3 libcurl4
libdebhelper-perl libedit2 libelf1 libevent-2.1-7 libevent-core-2.1-7
libevent-dev libevent-extra-2.1-7 libevent-openssl-2.1-7
libevent-pthreads-2.1-7 libexpat1 libfftw3-bin libfftw3-dev libfftw3-double3
libfftw3-single3 libfido2-1 libfile-stripnondeterminism-perl
libgfortran-9-dev libgfortran5 libglib2.0-0 libgssapi-krb5-2 libhwloc-dev
libhwloc-plugins libhwloc15 libibverbs-dev libibverbs1 libicu67 libjsoncpp1
libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack-dev liblapack3
libltdl-dev libltdl7 libmagic-mgc libmagic1 libmpdec2 libmpich-dev
libmpich12 libncurses6 libnghttp2-14 libnl-3-200 libnl-3-dev
libnl-route-3-200 libnl-route-3-dev libnuma-dev libnuma1 libopenmpi-dev
libopenmpi3 libpciaccess0 libpipeline1 libpmix2 libprocps8 libpsl5
libpthread-stubs0-dev libpython3-stdlib libpython3.8-minimal
libpython3.8-stdlib librhash0 librtmp1 libsigsegv2 libssh2-1
libsub-override-perl libtool libuchardet0 libuv1 libx11-6 libx11-data
libx11-dev libxau-dev libxau6 libxcb1 libxcb1-dev libxdmcp-dev libxdmcp6
libxext6 libxml2 libxnvctrl0 lsb-release m4 man-db mime-support mpich
ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client po-debconf
procps python3 python3-minimal python3.8 python3.8-minimal
sbuild-build-depends-gromacs-dummy sensible-utils x11proto-core-dev
x11proto-dev xorg-sgml-doctools xtrans-dev zlib1g-dev
0 upgraded, 133 newly installed, 0 to remove and 3 not upgraded.
Need to get 67.7 MB of archives.
After this operation, 362 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-vm1oud/apt_archive ./ sbuild-build-depends-gromacs-dummy 0.invalid.0 [952 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-5 [783 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.2-2 [29.6 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.9.3-2 [1269 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf libpython3.8-minimal armhf 3.8.4~rc1-1 [751 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf libexpat1 armhf 2.2.9-1 [71.5 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf python3.8-minimal armhf 3.8.4~rc1-1 [1629 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf python3-minimal armhf 3.8.2-3 [37.6 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf mime-support all 3.64 [37.8 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf libmpdec2 armhf 2.4.2-3 [68.1 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf libpython3.8-stdlib armhf 3.8.4~rc1-1 [1600 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf python3.8 armhf 3.8.4~rc1-1 [419 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf libpython3-stdlib armhf 3.8.2-3 [20.8 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf python3 armhf 3.8.2-3 [63.7 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf libncurses6 armhf 6.2-1 [79.5 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf libprocps8 armhf 2:3.3.16-5 [59.8 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf procps armhf 2:3.3.16-5 [238 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf sensible-utils all 0.0.12+nmu1 [16.0 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.38-5 [262 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.38-5 [113 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.38-5 [67.0 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.19.8.1-10 [117 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf libbsd0 armhf 0.10.0-1 [112 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf libedit2 armhf 3.1-20191231-1 [79.2 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf libcbor0 armhf 0.5.0+dfsg-2 [19.5 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf libfido2-1 armhf 1.4.0-2 [43.9 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf libkrb5support0 armhf 1.17-10 [61.7 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf libk5crypto3 armhf 1.17-10 [112 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf libkeyutils1 armhf 1.6.1-2 [14.5 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf libkrb5-3 armhf 1.17-10 [320 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf libgssapi-krb5-2 armhf 1.17-10 [135 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf openssh-client armhf 1:8.3p1-1 [783 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-4 [185 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-11.1 [341 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.2-3 [801 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.19.8.1-10 [435 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf chrpath armhf 0.16-2 [15.4 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf cmake-data all 3.16.3-3+rpi1 [1628 kB]
Get:42 http://172.17.0.1/private bullseye-staging/main armhf libicu67 armhf 67.1-2 [8286 kB]
Get:43 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.10+dfsg-5+b1 [593 kB]
Get:44 http://172.17.0.1/private bullseye-staging/main armhf libarchive13 armhf 3.4.3-1 [295 kB]
Get:45 http://172.17.0.1/private bullseye-staging/main armhf libbrotli1 armhf 1.0.7-6.1 [255 kB]
Get:46 http://172.17.0.1/private bullseye-staging/main armhf libnghttp2-14 armhf 1.41.0-2 [61.2 kB]
Get:47 http://172.17.0.1/private bullseye-staging/main armhf libpsl5 armhf 0.21.0-1.1 [54.2 kB]
Get:48 http://172.17.0.1/private bullseye-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b1 [54.3 kB]
Get:49 http://172.17.0.1/private bullseye-staging/main armhf libssh2-1 armhf 1.8.0-2.1 [126 kB]
Get:50 http://172.17.0.1/private bullseye-staging/main armhf libcurl4 armhf 7.68.0-1 [286 kB]
Get:51 http://172.17.0.1/private bullseye-staging/main armhf libjsoncpp1 armhf 1.7.4-3.1 [65.8 kB]
Get:52 http://172.17.0.1/private bullseye-staging/main armhf librhash0 armhf 1.3.9-1 [133 kB]
Get:53 http://172.17.0.1/private bullseye-staging/main armhf libuv1 armhf 1.38.0-3 [115 kB]
Get:54 http://172.17.0.1/private bullseye-staging/main armhf cmake armhf 3.16.3-3+rpi1 [2653 kB]
Get:55 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-14 [513 kB]
Get:56 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:57 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 13.2 [187 kB]
Get:58 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:59 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:60 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.9.0-1 [25.5 kB]
Get:61 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.9.0-1 [15.2 kB]
Get:62 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.176-1.1 [158 kB]
Get:63 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13-5 [142 kB]
Get:64 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.64.3-2 [1158 kB]
Get:65 http://172.17.0.1/private bullseye-staging/main armhf libcroco3 armhf 0.6.13-1 [133 kB]
Get:66 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.19.8.1-10 [1219 kB]
Get:67 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:68 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:69 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 13.2 [1007 kB]
Get:70 http://172.17.0.1/private bullseye-staging/main armhf distro-info-data all 0.44 [6620 B]
Get:71 http://172.17.0.1/private bullseye-staging/main armhf libgfortran5 armhf 10.1.0-4+rpi1 [231 kB]
Get:72 http://172.17.0.1/private bullseye-staging/main armhf libgfortran-9-dev armhf 9.3.0-14+rpi1 [278 kB]
Get:73 http://172.17.0.1/private bullseye-staging/main armhf gfortran-9 armhf 9.3.0-14+rpi1 [8112 kB]
Get:74 http://172.17.0.1/private bullseye-staging/main armhf gfortran armhf 4:9.2.1-3.1+rpi1 [1440 B]
Get:75 http://172.17.0.1/private bullseye-staging/main armhf libhwloc15 armhf 2.2.0+dfsg-3 [113 kB]
Get:76 http://172.17.0.1/private bullseye-staging/main armhf hwloc-nox armhf 2.2.0+dfsg-3 [149 kB]
Get:77 http://172.17.0.1/private bullseye-staging/main armhf libnl-3-200 armhf 3.4.0-1 [55.0 kB]
Get:78 http://172.17.0.1/private bullseye-staging/main armhf libnl-route-3-200 armhf 3.4.0-1 [132 kB]
Get:79 http://172.17.0.1/private bullseye-staging/main armhf libibverbs1 armhf 29.0-1 [47.5 kB]
Get:80 http://172.17.0.1/private bullseye-staging/main armhf ibverbs-providers armhf 29.0-1 [24.2 kB]
Get:81 http://172.17.0.1/private bullseye-staging/main armhf libblas3 armhf 3.9.0-2 [108 kB]
Get:82 http://172.17.0.1/private bullseye-staging/main armhf libblas-dev armhf 3.9.0-2 [113 kB]
Get:83 http://172.17.0.1/private bullseye-staging/main armhf libboost1.71-dev armhf 1.71.0-6+b1 [9099 kB]
Get:84 http://172.17.0.1/private bullseye-staging/main armhf libboost-dev armhf 1.71.0.3+b2 [4624 B]
Get:85 http://172.17.0.1/private bullseye-staging/main armhf libevent-2.1-7 armhf 2.1.11-stable-1 [165 kB]
Get:86 http://172.17.0.1/private bullseye-staging/main armhf libevent-core-2.1-7 armhf 2.1.11-stable-1 [124 kB]
Get:87 http://172.17.0.1/private bullseye-staging/main armhf libevent-extra-2.1-7 armhf 2.1.11-stable-1 [98.7 kB]
Get:88 http://172.17.0.1/private bullseye-staging/main armhf libevent-pthreads-2.1-7 armhf 2.1.11-stable-1 [54.7 kB]
Get:89 http://172.17.0.1/private bullseye-staging/main armhf libevent-openssl-2.1-7 armhf 2.1.11-stable-1 [59.7 kB]
Get:90 http://172.17.0.1/private bullseye-staging/main armhf libevent-dev armhf 2.1.11-stable-1 [279 kB]
Get:91 http://172.17.0.1/private bullseye-staging/main armhf libfftw3-double3 armhf 3.3.8-2 [429 kB]
Get:92 http://172.17.0.1/private bullseye-staging/main armhf libfftw3-single3 armhf 3.3.8-2 [633 kB]
Get:93 http://172.17.0.1/private bullseye-staging/main armhf libfftw3-bin armhf 3.3.8-2 [43.6 kB]
Get:94 http://172.17.0.1/private bullseye-staging/main armhf libfftw3-dev armhf 3.3.8-2 [1060 kB]
Get:95 http://172.17.0.1/private bullseye-staging/main armhf libnuma1 armhf 2.0.12-1 [22.5 kB]
Get:96 http://172.17.0.1/private bullseye-staging/main armhf libnuma-dev armhf 2.0.12-1 [35.6 kB]
Get:97 http://172.17.0.1/private bullseye-staging/main armhf libltdl7 armhf 2.4.6-14 [388 kB]
Get:98 http://172.17.0.1/private bullseye-staging/main armhf libltdl-dev armhf 2.4.6-14 [159 kB]
Get:99 http://172.17.0.1/private bullseye-staging/main armhf libhwloc-dev armhf 2.2.0+dfsg-3 [174 kB]
Get:100 http://172.17.0.1/private bullseye-staging/main armhf libpciaccess0 armhf 0.14-1 [51.0 kB]
Get:101 http://172.17.0.1/private bullseye-staging/main armhf libxau6 armhf 1:1.0.8-1+b2 [19.1 kB]
Get:102 http://172.17.0.1/private bullseye-staging/main armhf libxdmcp6 armhf 1:1.1.2-3 [25.0 kB]
Get:103 http://172.17.0.1/private bullseye-staging/main armhf libxcb1 armhf 1.14-2 [135 kB]
Get:104 http://172.17.0.1/private bullseye-staging/main armhf libx11-data all 2:1.6.9-2 [298 kB]
Get:105 http://172.17.0.1/private bullseye-staging/main armhf libx11-6 armhf 2:1.6.9-2 [692 kB]
Get:106 http://172.17.0.1/private bullseye-staging/main armhf libxext6 armhf 2:1.3.3-1+b2 [47.8 kB]
Get:107 http://172.17.0.1/private bullseye-staging/main armhf libxnvctrl0 armhf 440.100-1 [25.3 kB]
Get:108 http://172.17.0.1/private bullseye-staging/main armhf ocl-icd-libopencl1 armhf 2.2.12-4 [36.0 kB]
Get:109 http://172.17.0.1/private bullseye-staging/main armhf libhwloc-plugins armhf 2.2.0+dfsg-3 [19.0 kB]
Get:110 http://172.17.0.1/private bullseye-staging/main armhf libnl-3-dev armhf 3.4.0-1 [92.4 kB]
Get:111 http://172.17.0.1/private bullseye-staging/main armhf libnl-route-3-dev armhf 3.4.0-1 [145 kB]
Get:112 http://172.17.0.1/private bullseye-staging/main armhf libibverbs-dev armhf 29.0-1 [199 kB]
Get:113 http://172.17.0.1/private bullseye-staging/main armhf liblapack3 armhf 3.9.0-2 [1602 kB]
Get:114 http://172.17.0.1/private bullseye-staging/main armhf liblapack-dev armhf 3.9.0-2 [2981 kB]
Get:115 http://172.17.0.1/private bullseye-staging/main armhf libmpich12 armhf 3.4~a2+really3.3.2-1 [1057 kB]
Get:116 http://172.17.0.1/private bullseye-staging/main armhf mpich armhf 3.4~a2+really3.3.2-1 [335 kB]
Get:117 http://172.17.0.1/private bullseye-staging/main armhf libmpich-dev armhf 3.4~a2+really3.3.2-1 [1528 kB]
Get:118 http://172.17.0.1/private bullseye-staging/main armhf libpmix2 armhf 3.1.5-1+b1 [378 kB]
Get:119 http://172.17.0.1/private bullseye-staging/main armhf libopenmpi3 armhf 4.0.4-1+rpi1 [1689 kB]
Get:120 http://172.17.0.1/private bullseye-staging/main armhf openmpi-common all 4.0.4-1+rpi1 [173 kB]
Get:121 http://172.17.0.1/private bullseye-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [184 kB]
Get:122 http://172.17.0.1/private bullseye-staging/main armhf openmpi-bin armhf 4.0.4-1+rpi1 [189 kB]
Get:123 http://172.17.0.1/private bullseye-staging/main armhf libopenmpi-dev armhf 4.0.4-1+rpi1 [927 kB]
Get:124 http://172.17.0.1/private bullseye-staging/main armhf libpthread-stubs0-dev armhf 0.4-1 [5344 B]
Get:125 http://172.17.0.1/private bullseye-staging/main armhf xorg-sgml-doctools all 1:1.11-1 [21.9 kB]
Get:126 http://172.17.0.1/private bullseye-staging/main armhf x11proto-dev all 2020.1-1 [594 kB]
Get:127 http://172.17.0.1/private bullseye-staging/main armhf x11proto-core-dev all 2020.1-1 [3404 B]
Get:128 http://172.17.0.1/private bullseye-staging/main armhf libxau-dev armhf 1:1.0.8-1+b2 [22.4 kB]
Get:129 http://172.17.0.1/private bullseye-staging/main armhf libxdmcp-dev armhf 1:1.1.2-3 [40.9 kB]
Get:130 http://172.17.0.1/private bullseye-staging/main armhf xtrans-dev all 1.4.0-1 [98.7 kB]
Get:131 http://172.17.0.1/private bullseye-staging/main armhf libxcb1-dev armhf 1.14-2 [173 kB]
Get:132 http://172.17.0.1/private bullseye-staging/main armhf libx11-dev armhf 2:1.6.9-2 [766 kB]
Get:133 http://172.17.0.1/private bullseye-staging/main armhf lsb-release all 11.1.0+rpi1 [28.1 kB]
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Setting up libcbor0:armhf (0.5.0+dfsg-2) ...
Setting up libnghttp2-14:armhf (1.41.0-2) ...
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Setting up libkrb5support0:armhf (1.17-10) ...
Setting up xtrans-dev (1.4.0-1) ...
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Setting up libblas3:armhf (3.9.0-2) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode
Setting up libuv1:armhf (1.38.0-3) ...
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Setting up libgfortran5:armhf (10.1.0-4+rpi1) ...
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Setting up libmpich12:armhf (3.4~a2+really3.3.2-1) ...
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update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so to provide /usr/lib/arm-linux-gnueabihf/libblas.so (libblas.so-arm-linux-gnueabihf) in auto mode
Setting up libjsoncpp1:armhf (1.7.4-3.1) ...
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Setting up libxcb1:armhf (1.14-2) ...
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Setting up libedit2:armhf (3.1-20191231-1) ...
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Setting up libevent-openssl-2.1-7:armhf (2.1.11-stable-1) ...
Setting up m4 (1.4.18-4) ...
Setting up python3 (3.8.2-3) ...
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Setting up libevent-dev (2.1.11-stable-1) ...
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update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so to provide /usr/lib/arm-linux-gnueabihf/liblapack.so (liblapack.so-arm-linux-gnueabihf) in auto mode
Setting up libgssapi-krb5-2:armhf (1.17-10) ...
Setting up libcroco3:armhf (0.6.13-1) ...
Setting up autoconf (2.69-11.1) ...
Setting up dh-strip-nondeterminism (1.9.0-1) ...
Setting up dwz (0.13-5) ...
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Setting up groff-base (1.22.4-5) ...
Setting up procps (2:3.3.16-5) ...
update-alternatives: using /usr/bin/w.procps to provide /usr/bin/w (w) in auto mode
Setting up libcurl4:armhf (7.68.0-1) ...
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Setting up lsb-release (11.1.0+rpi1) ...
Setting up libfftw3-dev:armhf (3.3.8-2) ...
Setting up automake (1:1.16.2-3) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libibverbs1:armhf (29.0-1) ...
Setting up gettext (0.19.8.1-10) ...
Setting up libxcb1-dev:armhf (1.14-2) ...
Setting up gfortran-9 (9.3.0-14+rpi1) ...
Setting up ibverbs-providers:armhf (29.0-1) ...
Setting up mpich (3.4~a2+really3.3.2-1) ...
update-alternatives: using /usr/bin/mpicc.mpich to provide /usr/bin/mpicc (mpi) in auto mode
update-alternatives: using /usr/bin/mpirun.mpich to provide /usr/bin/mpirun (mpirun) in auto mode
Setting up openssh-client (1:8.3p1-1) ...
Setting up libx11-dev:armhf (2:1.6.9-2) ...
Setting up libxext6:armhf (2:1.3.3-1+b2) ...
Setting up man-db (2.9.3-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up gfortran (4:9.2.1-3.1+rpi1) ...
update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode
update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up libxnvctrl0:armhf (440.100-1) ...
Setting up libnl-route-3-dev:armhf (3.4.0-1) ...
Setting up libltdl-dev:armhf (2.4.6-14) ...
Setting up libmpich-dev:armhf (3.4~a2+really3.3.2-1) ...
update-alternatives: using /usr/include/arm-linux-gnueabihf/mpich to provide /usr/include/arm-linux-gnueabihf/mpi (mpi-arm-linux-gnueabihf) in auto mode
Setting up cmake (3.16.3-3+rpi1) ...
Setting up libhwloc-dev:armhf (2.2.0+dfsg-3) ...
Setting up po-debconf (1.0.21) ...
Setting up libibverbs-dev:armhf (29.0-1) ...
Setting up libhwloc-plugins:armhf (2.2.0+dfsg-3) ...
Setting up libpmix2:armhf (3.1.5-1+b1) ...
Setting up libopenmpi3:armhf (4.0.4-1+rpi1) ...
Setting up openmpi-bin (4.0.4-1+rpi1) ...
update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode
update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode
Setting up libopenmpi-dev:armhf (4.0.4-1+rpi1) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/openmpi/include to provide /usr/include/arm-linux-gnueabihf/mpi (mpi-arm-linux-gnueabihf) in auto mode
Setting up debhelper (13.2) ...
Setting up sbuild-build-depends-gromacs-dummy (0.invalid.0) ...
Setting up dh-autoreconf (19) ...
Processing triggers for libc-bin (2.30-8+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.6-armmp armhf (armv7l)
Toolchain package versions: binutils_2.34-8+rpi1 dpkg-dev_1.19.7 g++-9_9.3.0-14+rpi1 gcc-9_9.3.0-14+rpi1 libc6-dev_2.30-8+rpi1 libstdc++-9-dev_9.3.0-14+rpi1 libstdc++6_10.1.0-4+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2
Package versions: adduser_3.118 apt_2.1.6 autoconf_2.69-11.1 automake_1:1.16.2-3 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11+rpi1 base-passwd_3.5.47 bash_5.0-6 binutils_2.34-8+rpi1 binutils-arm-linux-gnueabihf_2.34-8+rpi1 binutils-common_2.34-8+rpi1 bsdextrautils_2.35.2-6 bsdutils_1:2.35.2-6 build-essential_12.8 bzip2_1.0.8-3 chrpath_0.16-2 cmake_3.16.3-3+rpi1 cmake-data_3.16.3-3+rpi1 coreutils_8.30-3 cpp_4:9.2.1-3.1+rpi1 cpp-9_9.3.0-14+rpi1 dash_0.5.10.2-7 debconf_1.5.74 debhelper_13.2 debianutils_4.9.1 dh-autoreconf_19 dh-strip-nondeterminism_1.9.0-1 diffutils_1:3.7-3 dirmngr_2.2.20-1 distro-info-data_0.44 dmsetup_2:1.02.167-1+b2 dpkg_1.19.7 dpkg-dev_1.19.7 dwz_0.13-5 e2fsprogs_1.45.6-1 fakeroot_1.24-1 file_1:5.38-5 findutils_4.7.0-1 g++_4:9.2.1-3.1+rpi1 g++-9_9.3.0-14+rpi1 gcc_4:9.2.1-3.1+rpi1 gcc-10-base_10.1.0-4+rpi1 gcc-6-base_6.5.0-1+rpi3 gcc-7-base_7.5.0-6+rpi1 gcc-8-base_8.4.0-4+rpi1 gcc-9_9.3.0-14+rpi1 gcc-9-base_9.3.0-14+rpi1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gfortran_4:9.2.1-3.1+rpi1 gfortran-9_9.3.0-14+rpi1 gnupg_2.2.20-1 gnupg-l10n_2.2.20-1 gnupg-utils_2.2.20-1 gpg_2.2.20-1 gpg-agent_2.2.20-1 gpg-wks-client_2.2.20-1 gpg-wks-server_2.2.20-1 gpgconf_2.2.20-1 gpgsm_2.2.20-1 gpgv_2.2.20-1 grep_3.4-1 groff-base_1.22.4-5 gzip_1.10-2 hostname_3.23 hwloc-nox_2.2.0+dfsg-3 ibverbs-providers_29.0-1 init-system-helpers_1.58 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-8 libapt-pkg6.0_2.1.6 libarchive-zip-perl_1.68-1 libarchive13_3.4.3-1 libargon2-1_0~20171227-0.2 libasan5_9.3.0-14+rpi1 libassuan0_2.5.3-7.1 libatomic1_10.1.0-4+rpi1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-3 libaudit1_1:2.8.5-3 libbinutils_2.34-8+rpi1 libblas-dev_3.9.0-2 libblas3_3.9.0-2 libblkid1_2.35.2-6 libboost-dev_1.71.0.3+b2 libboost1.71-dev_1.71.0-6+b1 libbrotli1_1.0.7-6.1 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-3 libc-bin_2.30-8+rpi1 libc-dev-bin_2.30-8+rpi1 libc6_2.30-8+rpi1 libc6-dev_2.30-8+rpi1 libcap-ng0_0.7.9-2.2 libcbor0_0.5.0+dfsg-2 libcc1-0_10.1.0-4+rpi1 libcom-err2_1.45.6-1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.16-1 libcrypt1_1:4.4.16-1 libcryptsetup12_2:2.3.3-1 libctf-nobfd0_2.34-8+rpi1 libctf0_2.34-8+rpi1 libcurl4_7.68.0-1 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.252 libdebhelper-perl_13.2 libdevmapper1.02.1_2:1.02.167-1+b2 libdpkg-perl_1.19.7 libedit2_3.1-20191231-1 libelf1_0.176-1.1 libevent-2.1-7_2.1.11-stable-1 libevent-core-2.1-7_2.1.11-stable-1 libevent-dev_2.1.11-stable-1 libevent-extra-2.1-7_2.1.11-stable-1 libevent-openssl-2.1-7_2.1.11-stable-1 libevent-pthreads-2.1-7_2.1.11-stable-1 libexpat1_2.2.9-1 libext2fs2_1.45.6-1 libfakeroot_1.24-1 libffi7_3.3-4 libfftw3-bin_3.3.8-2 libfftw3-dev_3.3.8-2 libfftw3-double3_3.3.8-2 libfftw3-single3_3.3.8-2 libfido2-1_1.4.0-2 libfile-stripnondeterminism-perl_1.9.0-1 libgcc-9-dev_9.3.0-14+rpi1 libgcc-s1_10.1.0-4+rpi1 libgcrypt20_1.8.5-5 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libgfortran-9-dev_9.3.0-14+rpi1 libgfortran5_10.1.0-4+rpi1 libglib2.0-0_2.64.3-2 libgmp10_2:6.2.0+dfsg-6 libgnutls30_3.6.14-2 libgomp1_10.1.0-4+rpi1 libgpg-error0_1.38-2 libgssapi-krb5-2_1.17-10 libhogweed5_3.5.1+really3.5.1-2 libhwloc-dev_2.2.0+dfsg-3 libhwloc-plugins_2.2.0+dfsg-3 libhwloc15_2.2.0+dfsg-3 libibverbs-dev_29.0-1 libibverbs1_29.0-1 libicu67_67.1-2 libidn2-0_2.3.0-1 libisl22_0.22.1-1 libjson-c4_0.13.1+dfsg-9 libjsoncpp1_1.7.4-3.1 libk5crypto3_1.17-10 libkeyutils1_1.6.1-2 libkrb5-3_1.17-10 libkrb5support0_1.17-10 libksba8_1.4.0-2 liblapack-dev_3.9.0-2 liblapack3_3.9.0-2 libldap-2.4-2_2.4.50+dfsg-1 libldap-common_2.4.50+dfsg-1 liblocale-gettext-perl_1.07-4 libltdl-dev_2.4.6-14 libltdl7_2.4.6-14 liblz4-1_1.9.2-2 liblzma5_5.2.4-1 libmagic-mgc_1:5.38-5 libmagic1_1:5.38-5 libmount1_2.35.2-6 libmpc3_1.1.0-1 libmpdec2_2.4.2-3 libmpfr6_4.0.2-1 libmpich-dev_3.4~a2+really3.3.2-1 libmpich12_3.4~a2+really3.3.2-1 libncurses6_6.2-1 libncursesw6_6.2-1 libnettle7_3.5.1+really3.5.1-2 libnghttp2-14_1.41.0-2 libnl-3-200_3.4.0-1 libnl-3-dev_3.4.0-1 libnl-route-3-200_3.4.0-1 libnl-route-3-dev_3.4.0-1 libnpth0_1.6-2 libnuma-dev_2.0.12-1 libnuma1_2.0.12-1 libopenmpi-dev_4.0.4-1+rpi1 libopenmpi3_4.0.4-1+rpi1 libp11-kit0_0.23.20-1 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpciaccess0_0.14-1 libpcre2-8-0_10.34-7 libpcre3_2:8.39-13 libperl5.30_5.30.3-4 libpipeline1_1.5.2-2 libpmix2_3.1.5-1+b1 libprocps8_2:3.3.16-5 libpsl5_0.21.0-1.1 libpthread-stubs0-dev_0.4-1 libpython3-stdlib_3.8.2-3 libpython3.8-minimal_3.8.4~rc1-1 libpython3.8-stdlib_3.8.4~rc1-1 libreadline8_8.0-4 librhash0_1.3.9-1 librtmp1_2.4+20151223.gitfa8646d.1-2+b1 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.4.3-1+rpi1 libselinux1_3.0-1+b1 libsemanage-common_3.0-1 libsemanage1_3.0-1+b1 libsepol1_3.0-1 libsigsegv2_2.12-2 libsmartcols1_2.35.2-6 libsqlite3-0_3.32.3-1 libss2_1.45.6-1 libssh2-1_1.8.0-2.1 libssl1.1_1.1.1g-1 libstdc++-9-dev_9.3.0-14+rpi1 libstdc++6_10.1.0-4+rpi1 libsub-override-perl_0.09-2 libsystemd0_245.6-2+rpi1 libtasn1-6_4.16.0-2 libtext-charwidth-perl_0.04-10 libtext-iconv-perl_1.7-7 libtinfo6_6.2-1 libtool_2.4.6-14 libubsan1_10.1.0-4+rpi1 libuchardet0_0.0.7-1 libudev1_245.6-2+rpi1 libunistring2_0.9.10-4 libuuid1_2.35.2-6 libuv1_1.38.0-3 libx11-6_2:1.6.9-2 libx11-data_2:1.6.9-2 libx11-dev_2:1.6.9-2 libxau-dev_1:1.0.8-1+b2 libxau6_1:1.0.8-1+b2 libxcb1_1.14-2 libxcb1-dev_1.14-2 libxdmcp-dev_1:1.1.2-3 libxdmcp6_1:1.1.2-3 libxext6_2:1.3.3-1+b2 libxml2_2.9.10+dfsg-5+b1 libxnvctrl0_440.100-1 libzstd1_1.4.5+dfsg-3+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2 login_1:4.8.1-1 logsave_1.45.6-1 lsb-base_11.1.0+rpi1 lsb-release_11.1.0+rpi1 m4_1.4.18-4 make_4.2.1-2 man-db_2.9.3-2 mawk_1.3.4.20200120-2 mime-support_3.64 mount_2.35.2-6 mpich_3.4~a2+really3.3.2-1 ncurses-base_6.2-1 ncurses-bin_6.2-1 netbase_6.1 ocl-icd-libopencl1_2.2.12-4 openmpi-bin_4.0.4-1+rpi1 openmpi-common_4.0.4-1+rpi1 openssh-client_1:8.3p1-1 passwd_1:4.8.1-1 patch_2.7.6-6 perl_5.30.3-4 perl-base_5.30.3-4 perl-modules-5.30_5.30.3-4 pinentry-curses_1.1.0-4 po-debconf_1.0.21 procps_2:3.3.16-5 python3_3.8.2-3 python3-minimal_3.8.2-3 python3.8_3.8.4~rc1-1 python3.8-minimal_3.8.4~rc1-1 raspbian-archive-keyring_20120528.2 readline-common_8.0-4 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-gromacs-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sysvinit-utils_2.96-3 tar_1.30+dfsg-7 tzdata_2020a-1 util-linux_2.35.2-6 x11proto-core-dev_2020.1-1 x11proto-dev_2020.1-1 xorg-sgml-doctools_1:1.11-1 xtrans-dev_1.4.0-1 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-2 zlib1g-dev_1:1.2.11.dfsg-2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Fri Jul 10 04:22:53 2020 UTC
gpgv: using RSA key 843E5FA61E6063389876D2E5EE4AFD69EC65108F
gpgv: issuer "nbreen@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./gromacs_2020.3-1.dsc
dpkg-source: info: extracting gromacs in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking gromacs_2020.3.orig.tar.gz
dpkg-source: info: unpacking gromacs_2020.3-1.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying arm64-disable-numa-test.patch
dpkg-source: info: applying readme.patch
dpkg-source: info: applying copyright-file.patch
dpkg-source: info: applying disable-cpuinfotest.patch
dpkg-source: info: applying mdrun-test-timeout.patch
dpkg-source: info: applying local-mathjax.patch
dpkg-source: info: applying mpi-tests-localhost.patch
Check disc space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=bullseye-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bullseye-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-ed0524e9-90c0-451f-87b1-c0a5cca4714b
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package gromacs
dpkg-buildpackage: info: source version 2020.3-1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh_testdir
dh_testroot
rm -rf build docs/doxygen/*.pyc
dh_clean build-basic build-mpich build-openmpi build-manual configure-stamp \
debian/gromacs-mpich.README.Debian debian/gromacs-openmpi.README.Debian
debian/rules binary-arch
dh_testdir
(mkdir -p build/basic; cd build/basic; cmake /<<PKGBUILDDIR>> -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_VERSION_STRING_OF_FORK="Raspbian-2020.3-1" -DGMX_GIT_VERSION_INFO=OFF -DGMX_SIMD=None -DGMX_MPI=OFF -DGMX_X11=ON -DBUILD_SHARED_LIBS=ON -DGMX_INSTALL_LEGACY_API=ON)
-- The C compiler identification is GNU 9.3.0
-- The CXX compiler identification is GNU 9.3.0
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Looking for NVIDIA GPUs present in the system
-- Could not detect NVIDIA GPUs
-- No compatible CUDA toolkit found (v5.0+), disabling native GPU acceleration
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- Performing Test CFLAGS_EXCESS_PREC
-- Performing Test CFLAGS_EXCESS_PREC - Success
-- Performing Test CFLAGS_COPT
-- Performing Test CFLAGS_COPT - Success
-- Performing Test CFLAGS_NOINLINE
-- Performing Test CFLAGS_NOINLINE - Success
-- Performing Test CXXFLAGS_EXCESS_PREC
-- Performing Test CXXFLAGS_EXCESS_PREC - Success
-- Performing Test CXXFLAGS_COPT
-- Performing Test CXXFLAGS_COPT - Success
-- Performing Test CXXFLAGS_NOINLINE
-- Performing Test CXXFLAGS_NOINLINE - Success
-- Looking for include file unistd.h
-- Looking for include file unistd.h - found
-- Looking for include file pwd.h
-- Looking for include file pwd.h - found
-- Looking for include file dirent.h
-- Looking for include file dirent.h - found
-- Looking for include file time.h
-- Looking for include file time.h - found
-- Looking for include file sys/time.h
-- Looking for include file sys/time.h - found
-- Looking for include file io.h
-- Looking for include file io.h - not found
-- Looking for include file sched.h
-- Looking for include file sched.h - found
-- Looking for include file xmmintrin.h
-- Looking for include file xmmintrin.h - not found
-- Looking for gettimeofday
-- Looking for gettimeofday - found
-- Looking for sysconf
-- Looking for sysconf - found
-- Looking for nice
-- Looking for nice - found
-- Looking for fsync
-- Looking for fsync - found
-- Looking for _fileno
-- Looking for _fileno - not found
-- Looking for fileno
-- Looking for fileno - found
-- Looking for _commit
-- Looking for _commit - not found
-- Looking for sigaction
-- Looking for sigaction - found
-- Performing Test HAVE_BUILTIN_CLZ
-- Performing Test HAVE_BUILTIN_CLZ - Success
-- Performing Test HAVE_BUILTIN_CLZLL
-- Performing Test HAVE_BUILTIN_CLZLL - Success
-- Looking for clock_gettime in rt
-- Looking for clock_gettime in rt - found
-- Looking for feenableexcept in m
-- Looking for feenableexcept in m - found
-- Looking for fedisableexcept in m
-- Looking for fedisableexcept in m - found
-- Checking for sched.h GNU affinity API
-- Performing Test sched_affinity_compile
-- Performing Test sched_affinity_compile - Success
-- Looking for include file mm_malloc.h
-- Looking for include file mm_malloc.h - not found
-- Looking for include file malloc.h
-- Looking for include file malloc.h - found
-- Checking for _mm_malloc()
-- Checking for _mm_malloc() - not supported
-- Looking for posix_memalign
-- Looking for posix_memalign - found
-- Looking for memalign
-- Looking for memalign - not found
-- Check if the system is big endian
-- Searching 16 bit integer
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of unsigned short
-- Check size of unsigned short - done
-- Using unsigned short
-- Check if the system is big endian - little endian
-- Looking for HWLOC
-- Looking for hwloc_topology_init
-- Looking for hwloc_topology_init - found
-- hwloc version:
-- Found HWLOC: /usr/lib/arm-linux-gnueabihf/libhwloc.so (found suitable version "2.2.0", minimum required is "1.5")
-- Found X11: /usr/include
-- Looking for XOpenDisplay in /usr/lib/arm-linux-gnueabihf/libX11.so
-- Looking for XOpenDisplay in /usr/lib/arm-linux-gnueabihf/libX11.so - found
-- Looking for gethostbyname
-- Looking for gethostbyname - found
-- Looking for connect
-- Looking for connect - found
-- Looking for remove
-- Looking for remove - found
-- Looking for shmat
-- Looking for shmat - found
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Looking for C++ include pthread.h
-- Looking for C++ include pthread.h - found
-- Atomic operations found
-- Performing Test PTHREAD_SETAFFINITY
-- Performing Test PTHREAD_SETAFFINITY - Success
-- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.11")
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so - found
-- Checking for GCC x86 inline asm
-- Checking for GCC x86 inline asm - not supported
-- Detected build CPU vendor - ARM
-- Detected build CPU brand - ARMv7 Processor rev 10 (v7l)
-- Detected build CPU family - 7
-- Detected build CPU model - 2
-- Detected build CPU stepping - 10
-- Detected build CPU features - neon
-- Disabling RDTSCP support
-- Checking for 64-bit off_t
-- Checking for 64-bit off_t - present with _FILE_OFFSET_BITS=64
-- Checking for fseeko/ftello
-- Checking for fseeko/ftello - present
-- Checking for SIGUSR1
-- Checking for SIGUSR1 - found
-- Checking for pipe support
-- Checking for system XDR support
-- Checking for system XDR support - present
-- SIMD instructions disabled
-- Performing Test _callconv___vectorcall
-- Performing Test _callconv___vectorcall - Failed
-- Performing Test _callconv___regcall
-- Performing Test _callconv___regcall - Failed
-- Performing Test _callconv_
-- Performing Test _callconv_ - Success
-- pkg-config could not detect fftw3f, trying generic detection
-- Looking for fftwf_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Looking for fftwf_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Looking for fftwf_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Looking for fftwf_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Using external FFT library - FFTW3
-- Looking for sgemm_
-- Looking for sgemm_ - not found
-- Looking for sgemm_
-- Looking for sgemm_ - found
-- Found BLAS: /usr/lib/arm-linux-gnueabihf/libblas.so
-- Looking for cheev_
-- Looking for cheev_ - not found
-- Looking for cheev_
-- Looking for cheev_ - found
-- A library with LAPACK API found.
-- Checking for dlopen
-- Performing Test HAVE_DLOPEN
-- Performing Test HAVE_DLOPEN - Success
-- Checking for dlopen - found
-- Using dynamic plugins (e.g VMD-supported file formats)
-- Checking for suitable VMD version
-- VMD plugins not found. Path to VMD can be set with VMDDIR.
-- Using default binary suffix: ""
-- Using default library suffix: ""
-- Could not convert sample image, ImageMagick convert can not be used. A possible way to fix it can be found here: https://alexvanderbist.com/posts/2018/fixing-imagick-error-unauthorized
Traceback (most recent call last):
File "<string>", line 1, in <module>
ModuleNotFoundError: No module named 'pygments'
-- Could NOT find Sphinx (missing: SPHINX_EXECUTABLE pygments) (Required is at least version "1.6.1")
-- Performing Test HAVE_NO_DEPRECATED_COPY
-- Performing Test HAVE_NO_DEPRECATED_COPY - Success
-- Performing Test HAS_NO_STRINGOP_TRUNCATION
-- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success
-- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION
-- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION - Success
-- Performing Test HAS_NO_REDUNDANT_MOVE
-- Performing Test HAS_NO_REDUNDANT_MOVE - Success
-- Performing Test HAS_NO_UNUSED
-- Performing Test HAS_NO_UNUSED - Success
-- Performing Test HAS_NO_UNUSED_PARAMETER
-- Performing Test HAS_NO_UNUSED_PARAMETER - Success
-- Performing Test HAS_NO_MISSING_DECLARATIONS
-- Performing Test HAS_NO_MISSING_DECLARATIONS - Success
-- Performing Test HAS_NO_NULL_CONVERSIONS
-- Performing Test HAS_NO_NULL_CONVERSIONS - Success
-- Performing Test HAS_DECL_IN_SOURCE
-- Performing Test HAS_DECL_IN_SOURCE - Failed
-- Performing Test HAS_NO_CLASS_MEMACCESS
-- Performing Test HAS_NO_CLASS_MEMACCESS - Success
-- Check if the system is big endian
-- Searching 16 bit integer
-- Using unsigned short
-- Check if the system is big endian - little endian
-- Looking for inttypes.h
-- Looking for inttypes.h - found
-- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE)
-- Doxygen not found. Documentation targets will not be generated.
-- Configuring done
-- Generating done
-- Build files have been written to: /<<PKGBUILDDIR>>/build/basic
(mkdir -p build/basic-dp; cd build/basic-dp; cmake /<<PKGBUILDDIR>> -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_VERSION_STRING_OF_FORK="Raspbian-2020.3-1" -DGMX_GIT_VERSION_INFO=OFF -DGMX_SIMD=None -DGMX_MPI=OFF -DGMX_X11=ON -DBUILD_SHARED_LIBS=ON -DGMX_DOUBLE=ON)
-- The C compiler identification is GNU 9.3.0
-- The CXX compiler identification is GNU 9.3.0
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
CMake Warning at cmake/gmxManageGPU.cmake:53 (message):
GPU acceleration is not available in double precision, disabled!
Call Stack (most recent call first):
CMakeLists.txt:217 (include)
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- Performing Test CFLAGS_EXCESS_PREC
-- Performing Test CFLAGS_EXCESS_PREC - Success
-- Performing Test CFLAGS_COPT
-- Performing Test CFLAGS_COPT - Success
-- Performing Test CFLAGS_NOINLINE
-- Performing Test CFLAGS_NOINLINE - Success
-- Performing Test CXXFLAGS_EXCESS_PREC
-- Performing Test CXXFLAGS_EXCESS_PREC - Success
-- Performing Test CXXFLAGS_COPT
-- Performing Test CXXFLAGS_COPT - Success
-- Performing Test CXXFLAGS_NOINLINE
-- Performing Test CXXFLAGS_NOINLINE - Success
-- Looking for include file unistd.h
-- Looking for include file unistd.h - found
-- Looking for include file pwd.h
-- Looking for include file pwd.h - found
-- Looking for include file dirent.h
-- Looking for include file dirent.h - found
-- Looking for include file time.h
-- Looking for include file time.h - found
-- Looking for include file sys/time.h
-- Looking for include file sys/time.h - found
-- Looking for include file io.h
-- Looking for include file io.h - not found
-- Looking for include file sched.h
-- Looking for include file sched.h - found
-- Looking for include file xmmintrin.h
-- Looking for include file xmmintrin.h - not found
-- Looking for gettimeofday
-- Looking for gettimeofday - found
-- Looking for sysconf
-- Looking for sysconf - found
-- Looking for nice
-- Looking for nice - found
-- Looking for fsync
-- Looking for fsync - found
-- Looking for _fileno
-- Looking for _fileno - not found
-- Looking for fileno
-- Looking for fileno - found
-- Looking for _commit
-- Looking for _commit - not found
-- Looking for sigaction
-- Looking for sigaction - found
-- Performing Test HAVE_BUILTIN_CLZ
-- Performing Test HAVE_BUILTIN_CLZ - Success
-- Performing Test HAVE_BUILTIN_CLZLL
-- Performing Test HAVE_BUILTIN_CLZLL - Success
-- Looking for clock_gettime in rt
-- Looking for clock_gettime in rt - found
-- Looking for feenableexcept in m
-- Looking for feenableexcept in m - found
-- Looking for fedisableexcept in m
-- Looking for fedisableexcept in m - found
-- Checking for sched.h GNU affinity API
-- Performing Test sched_affinity_compile
-- Performing Test sched_affinity_compile - Success
-- Looking for include file mm_malloc.h
-- Looking for include file mm_malloc.h - not found
-- Looking for include file malloc.h
-- Looking for include file malloc.h - found
-- Checking for _mm_malloc()
-- Checking for _mm_malloc() - not supported
-- Looking for posix_memalign
-- Looking for posix_memalign - found
-- Looking for memalign
-- Looking for memalign - not found
-- Check if the system is big endian
-- Searching 16 bit integer
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of unsigned short
-- Check size of unsigned short - done
-- Using unsigned short
-- Check if the system is big endian - little endian
-- Looking for HWLOC
-- Looking for hwloc_topology_init
-- Looking for hwloc_topology_init - found
-- hwloc version:
-- Found HWLOC: /usr/lib/arm-linux-gnueabihf/libhwloc.so (found suitable version "2.2.0", minimum required is "1.5")
-- Found X11: /usr/include
-- Looking for XOpenDisplay in /usr/lib/arm-linux-gnueabihf/libX11.so
-- Looking for XOpenDisplay in /usr/lib/arm-linux-gnueabihf/libX11.so - found
-- Looking for gethostbyname
-- Looking for gethostbyname - found
-- Looking for connect
-- Looking for connect - found
-- Looking for remove
-- Looking for remove - found
-- Looking for shmat
-- Looking for shmat - found
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Looking for C++ include pthread.h
-- Looking for C++ include pthread.h - found
-- Atomic operations found
-- Performing Test PTHREAD_SETAFFINITY
-- Performing Test PTHREAD_SETAFFINITY - Success
-- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.11")
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so - found
-- Checking for GCC x86 inline asm
-- Checking for GCC x86 inline asm - not supported
-- Detected build CPU vendor - ARM
-- Detected build CPU brand - ARMv7 Processor rev 10 (v7l)
-- Detected build CPU family - 7
-- Detected build CPU model - 2
-- Detected build CPU stepping - 10
-- Detected build CPU features - neon
-- Disabling RDTSCP support
-- Checking for 64-bit off_t
-- Checking for 64-bit off_t - present with _FILE_OFFSET_BITS=64
-- Checking for fseeko/ftello
-- Checking for fseeko/ftello - present
-- Checking for SIGUSR1
-- Checking for SIGUSR1 - found
-- Checking for pipe support
-- Checking for system XDR support
-- Checking for system XDR support - present
-- SIMD instructions disabled
-- Performing Test _callconv___vectorcall
-- Performing Test _callconv___vectorcall - Failed
-- Performing Test _callconv___regcall
-- Performing Test _callconv___regcall - Failed
-- Performing Test _callconv_
-- Performing Test _callconv_ - Success
-- pkg-config could not detect fftw3, trying generic detection
-- Looking for fftw_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found
-- Looking for fftw_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found
-- Looking for fftw_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found
-- Looking for fftw_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_vsx in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_vsx in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Using external FFT library - FFTW3
-- Looking for sgemm_
-- Looking for sgemm_ - not found
-- Looking for sgemm_
-- Looking for sgemm_ - found
-- Found BLAS: /usr/lib/arm-linux-gnueabihf/libblas.so
-- Looking for cheev_
-- Looking for cheev_ - not found
-- Looking for cheev_
-- Looking for cheev_ - found
-- A library with LAPACK API found.
-- Checking for dlopen
-- Performing Test HAVE_DLOPEN
-- Performing Test HAVE_DLOPEN - Success
-- Checking for dlopen - found
-- Using dynamic plugins (e.g VMD-supported file formats)
-- Checking for suitable VMD version
-- VMD plugins not found. Path to VMD can be set with VMDDIR.
-- Using default binary suffix: "_d"
-- Using default library suffix: "_d"
-- Could not convert sample image, ImageMagick convert can not be used. A possible way to fix it can be found here: https://alexvanderbist.com/posts/2018/fixing-imagick-error-unauthorized
Traceback (most recent call last):
File "<string>", line 1, in <module>
ModuleNotFoundError: No module named 'pygments'
-- Could NOT find Sphinx (missing: SPHINX_EXECUTABLE pygments) (Required is at least version "1.6.1")
-- Performing Test HAVE_NO_DEPRECATED_COPY
-- Performing Test HAVE_NO_DEPRECATED_COPY - Success
-- Performing Test HAS_NO_STRINGOP_TRUNCATION
-- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success
-- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION
-- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION - Success
-- Performing Test HAS_NO_REDUNDANT_MOVE
-- Performing Test HAS_NO_REDUNDANT_MOVE - Success
-- Performing Test HAS_NO_UNUSED
-- Performing Test HAS_NO_UNUSED - Success
-- Performing Test HAS_NO_UNUSED_PARAMETER
-- Performing Test HAS_NO_UNUSED_PARAMETER - Success
-- Performing Test HAS_NO_MISSING_DECLARATIONS
-- Performing Test HAS_NO_MISSING_DECLARATIONS - Success
-- Performing Test HAS_NO_NULL_CONVERSIONS
-- Performing Test HAS_NO_NULL_CONVERSIONS - Success
-- Performing Test HAS_DECL_IN_SOURCE
-- Performing Test HAS_DECL_IN_SOURCE - Failed
-- Performing Test HAS_NO_CLASS_MEMACCESS
-- Performing Test HAS_NO_CLASS_MEMACCESS - Success
-- Check if the system is big endian
-- Searching 16 bit integer
-- Using unsigned short
-- Check if the system is big endian - little endian
-- Looking for inttypes.h
-- Looking for inttypes.h - found
-- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE)
-- Doxygen not found. Documentation targets will not be generated.
-- Configuring done
-- Generating done
-- Build files have been written to: /<<PKGBUILDDIR>>/build/basic-dp
(mkdir -p build/mpich; cd build/mpich; CC=/usr/bin/mpicc.mpich CXX=/usr/bin/mpicxx.mpich cmake \
/<<PKGBUILDDIR>> -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_VERSION_STRING_OF_FORK="Raspbian-2020.3-1" -DGMX_GIT_VERSION_INFO=OFF -DGMX_SIMD=None -DGMX_MPI=ON -DGMX_X11=OFF -DGMX_DEFAULT_SUFFIX=OFF -DMPIEXEC="/usr/bin/mpiexec.mpich" -DGMX_BUILD_MDRUN_ONLY=ON -DGMX_BINARY_SUFFIX="_mpi.mpich" -DGMX_LIBS_SUFFIX="_mpi.mpich")
-- The C compiler identification is GNU 9.3.0
-- The CXX compiler identification is GNU 9.3.0
-- Check for working C compiler: /usr/bin/mpicc.mpich
-- Check for working C compiler: /usr/bin/mpicc.mpich -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/mpicxx.mpich
-- Check for working CXX compiler: /usr/bin/mpicxx.mpich -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Looking for NVIDIA GPUs present in the system
-- Could not detect NVIDIA GPUs
-- No compatible CUDA toolkit found (v5.0+), disabling native GPU acceleration
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- Performing Test CFLAGS_EXCESS_PREC
-- Performing Test CFLAGS_EXCESS_PREC - Success
-- Performing Test CFLAGS_COPT
-- Performing Test CFLAGS_COPT - Success
-- Performing Test CFLAGS_NOINLINE
-- Performing Test CFLAGS_NOINLINE - Success
-- Performing Test CXXFLAGS_EXCESS_PREC
-- Performing Test CXXFLAGS_EXCESS_PREC - Success
-- Performing Test CXXFLAGS_COPT
-- Performing Test CXXFLAGS_COPT - Success
-- Performing Test CXXFLAGS_NOINLINE
-- Performing Test CXXFLAGS_NOINLINE - Success
-- Looking for include file unistd.h
-- Looking for include file unistd.h - found
-- Looking for include file pwd.h
-- Looking for include file pwd.h - found
-- Looking for include file dirent.h
-- Looking for include file dirent.h - found
-- Looking for include file time.h
-- Looking for include file time.h - found
-- Looking for include file sys/time.h
-- Looking for include file sys/time.h - found
-- Looking for include file io.h
-- Looking for include file io.h - not found
-- Looking for include file sched.h
-- Looking for include file sched.h - found
-- Looking for include file xmmintrin.h
-- Looking for include file xmmintrin.h - not found
-- Looking for gettimeofday
-- Looking for gettimeofday - found
-- Looking for sysconf
-- Looking for sysconf - found
-- Looking for nice
-- Looking for nice - found
-- Looking for fsync
-- Looking for fsync - found
-- Looking for _fileno
-- Looking for _fileno - not found
-- Looking for fileno
-- Looking for fileno - found
-- Looking for _commit
-- Looking for _commit - not found
-- Looking for sigaction
-- Looking for sigaction - found
-- Performing Test HAVE_BUILTIN_CLZ
-- Performing Test HAVE_BUILTIN_CLZ - Success
-- Performing Test HAVE_BUILTIN_CLZLL
-- Performing Test HAVE_BUILTIN_CLZLL - Success
-- Looking for clock_gettime in rt
-- Looking for clock_gettime in rt - found
-- Looking for feenableexcept in m
-- Looking for feenableexcept in m - found
-- Looking for fedisableexcept in m
-- Looking for fedisableexcept in m - found
-- Checking for sched.h GNU affinity API
-- Performing Test sched_affinity_compile
-- Performing Test sched_affinity_compile - Success
-- Looking for include file mm_malloc.h
-- Looking for include file mm_malloc.h - not found
-- Looking for include file malloc.h
-- Looking for include file malloc.h - found
-- Checking for _mm_malloc()
-- Checking for _mm_malloc() - not supported
-- Looking for posix_memalign
-- Looking for posix_memalign - found
-- Looking for memalign
-- Looking for memalign - not found
-- Check if the system is big endian
-- Searching 16 bit integer
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of unsigned short
-- Check size of unsigned short - done
-- Using unsigned short
-- Check if the system is big endian - little endian
-- MPI is not compatible with thread-MPI. Disabling thread-MPI.
-- Checking for MPI_IN_PLACE
-- Performing Test MPI_IN_PLACE_COMPILE_OK
-- Performing Test MPI_IN_PLACE_COMPILE_OK - Success
-- Checking for MPI_IN_PLACE - yes
-- Defaulting to building static libraries
-- Looking for HWLOC
-- Looking for hwloc_topology_init
-- Looking for hwloc_topology_init - found
-- hwloc version:
-- Found HWLOC: /usr/lib/arm-linux-gnueabihf/libhwloc.so (found suitable version "2.2.0", minimum required is "1.5")
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Looking for C++ include pthread.h
-- Looking for C++ include pthread.h - found
-- Atomic operations found
-- Performing Test PTHREAD_SETAFFINITY
-- Performing Test PTHREAD_SETAFFINITY - Success
-- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.11")
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so - found
-- Checking for GCC x86 inline asm
-- Checking for GCC x86 inline asm - not supported
-- Detected build CPU vendor - ARM
-- Detected build CPU brand - ARMv7 Processor rev 10 (v7l)
-- Detected build CPU family - 7
-- Detected build CPU model - 2
-- Detected build CPU stepping - 10
-- Detected build CPU features - neon
-- Disabling RDTSCP support
-- Checking for 64-bit off_t
-- Checking for 64-bit off_t - present with _FILE_OFFSET_BITS=64
-- Checking for fseeko/ftello
-- Checking for fseeko/ftello - present
-- Checking for SIGUSR1
-- Checking for SIGUSR1 - found
-- Checking for pipe support
-- Checking for system XDR support
-- Checking for system XDR support - present
-- SIMD instructions disabled
-- Performing Test _callconv___vectorcall
-- Performing Test _callconv___vectorcall - Failed
-- Performing Test _callconv___regcall
-- Performing Test _callconv___regcall - Failed
-- Performing Test _callconv_
-- Performing Test _callconv_ - Success
-- pkg-config could not detect fftw3f, trying generic detection
-- Looking for fftwf_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Looking for fftwf_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Looking for fftwf_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Looking for fftwf_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Using external FFT library - FFTW3
-- Looking for sgemm_
-- Looking for sgemm_ - not found
-- Looking for sgemm_
-- Looking for sgemm_ - found
-- Found BLAS: /usr/lib/arm-linux-gnueabihf/libblas.so
-- Looking for cheev_
-- Looking for cheev_ - not found
-- Looking for cheev_
-- Looking for cheev_ - found
-- A library with LAPACK API found.
-- Checking for dlopen
-- Performing Test HAVE_DLOPEN
-- Performing Test HAVE_DLOPEN - Success
-- Checking for dlopen - found
-- GROMACS only supports plugins in a build that uses shared libraries, which can be disabled for various reasons. BUILD_SHARED_LIBS=on and a toolchain that supports dynamic linking is required. (Hint: GMX_PREFER_STATIC_LIBS and GMX_BUILD_MDRUN_ONLY can influence the default BUILD_SHARED_LIBS, so if you need plugins, reconsider those choices.)
-- Not using dynamic plugins (e.g VMD-supported file formats)
-- Using manually set binary suffix: "_mpi.mpich"
-- Using manually set library suffix: "_mpi.mpich"
-- Performing Test HAVE_NO_DEPRECATED_COPY
-- Performing Test HAVE_NO_DEPRECATED_COPY - Success
-- Performing Test HAS_NO_STRINGOP_TRUNCATION
-- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success
-- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION
-- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION - Success
-- Performing Test HAS_NO_REDUNDANT_MOVE
-- Performing Test HAS_NO_REDUNDANT_MOVE - Success
-- Performing Test HAS_NO_UNUSED
-- Performing Test HAS_NO_UNUSED - Success
-- Performing Test HAS_NO_UNUSED_PARAMETER
-- Performing Test HAS_NO_UNUSED_PARAMETER - Success
-- Performing Test HAS_NO_MISSING_DECLARATIONS
-- Performing Test HAS_NO_MISSING_DECLARATIONS - Success
-- Performing Test HAS_NO_NULL_CONVERSIONS
-- Performing Test HAS_NO_NULL_CONVERSIONS - Success
-- Performing Test HAS_DECL_IN_SOURCE
-- Performing Test HAS_DECL_IN_SOURCE - Failed
-- Performing Test HAS_NO_CLASS_MEMACCESS
-- Performing Test HAS_NO_CLASS_MEMACCESS - Success
-- Check if the system is big endian
-- Searching 16 bit integer
-- Using unsigned short
-- Check if the system is big endian - little endian
-- Looking for inttypes.h
-- Looking for inttypes.h - found
-- Configuring done
-- Generating done
-- Build files have been written to: /<<PKGBUILDDIR>>/build/mpich
(mkdir -p build/mpich-dp; cd build/mpich-dp; CC=/usr/bin/mpicc.mpich CXX=/usr/bin/mpicxx.mpich cmake \
/<<PKGBUILDDIR>> -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_VERSION_STRING_OF_FORK="Raspbian-2020.3-1" -DGMX_GIT_VERSION_INFO=OFF -DGMX_SIMD=None -DGMX_MPI=ON -DGMX_X11=OFF -DGMX_DEFAULT_SUFFIX=OFF -DMPIEXEC="/usr/bin/mpiexec.mpich" -DGMX_BUILD_MDRUN_ONLY=ON -DGMX_DOUBLE=ON -DGMX_BINARY_SUFFIX="_mpi_d.mpich" -DGMX_LIBS_SUFFIX="_mpi_d.mpich")
-- The C compiler identification is GNU 9.3.0
-- The CXX compiler identification is GNU 9.3.0
-- Check for working C compiler: /usr/bin/mpicc.mpich
-- Check for working C compiler: /usr/bin/mpicc.mpich -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/mpicxx.mpich
-- Check for working CXX compiler: /usr/bin/mpicxx.mpich -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
CMake Warning at cmake/gmxManageGPU.cmake:53 (message):
GPU acceleration is not available in double precision, disabled!
Call Stack (most recent call first):
CMakeLists.txt:217 (include)
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- Performing Test CFLAGS_EXCESS_PREC
-- Performing Test CFLAGS_EXCESS_PREC - Success
-- Performing Test CFLAGS_COPT
-- Performing Test CFLAGS_COPT - Success
-- Performing Test CFLAGS_NOINLINE
-- Performing Test CFLAGS_NOINLINE - Success
-- Performing Test CXXFLAGS_EXCESS_PREC
-- Performing Test CXXFLAGS_EXCESS_PREC - Success
-- Performing Test CXXFLAGS_COPT
-- Performing Test CXXFLAGS_COPT - Success
-- Performing Test CXXFLAGS_NOINLINE
-- Performing Test CXXFLAGS_NOINLINE - Success
-- Looking for include file unistd.h
-- Looking for include file unistd.h - found
-- Looking for include file pwd.h
-- Looking for include file pwd.h - found
-- Looking for include file dirent.h
-- Looking for include file dirent.h - found
-- Looking for include file time.h
-- Looking for include file time.h - found
-- Looking for include file sys/time.h
-- Looking for include file sys/time.h - found
-- Looking for include file io.h
-- Looking for include file io.h - not found
-- Looking for include file sched.h
-- Looking for include file sched.h - found
-- Looking for include file xmmintrin.h
-- Looking for include file xmmintrin.h - not found
-- Looking for gettimeofday
-- Looking for gettimeofday - found
-- Looking for sysconf
-- Looking for sysconf - found
-- Looking for nice
-- Looking for nice - found
-- Looking for fsync
-- Looking for fsync - found
-- Looking for _fileno
-- Looking for _fileno - not found
-- Looking for fileno
-- Looking for fileno - found
-- Looking for _commit
-- Looking for _commit - not found
-- Looking for sigaction
-- Looking for sigaction - found
-- Performing Test HAVE_BUILTIN_CLZ
-- Performing Test HAVE_BUILTIN_CLZ - Success
-- Performing Test HAVE_BUILTIN_CLZLL
-- Performing Test HAVE_BUILTIN_CLZLL - Success
-- Looking for clock_gettime in rt
-- Looking for clock_gettime in rt - found
-- Looking for feenableexcept in m
-- Looking for feenableexcept in m - found
-- Looking for fedisableexcept in m
-- Looking for fedisableexcept in m - found
-- Checking for sched.h GNU affinity API
-- Performing Test sched_affinity_compile
-- Performing Test sched_affinity_compile - Success
-- Looking for include file mm_malloc.h
-- Looking for include file mm_malloc.h - not found
-- Looking for include file malloc.h
-- Looking for include file malloc.h - found
-- Checking for _mm_malloc()
-- Checking for _mm_malloc() - not supported
-- Looking for posix_memalign
-- Looking for posix_memalign - found
-- Looking for memalign
-- Looking for memalign - not found
-- Check if the system is big endian
-- Searching 16 bit integer
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of unsigned short
-- Check size of unsigned short - done
-- Using unsigned short
-- Check if the system is big endian - little endian
-- MPI is not compatible with thread-MPI. Disabling thread-MPI.
-- Checking for MPI_IN_PLACE
-- Performing Test MPI_IN_PLACE_COMPILE_OK
-- Performing Test MPI_IN_PLACE_COMPILE_OK - Success
-- Checking for MPI_IN_PLACE - yes
-- Defaulting to building static libraries
-- Looking for HWLOC
-- Looking for hwloc_topology_init
-- Looking for hwloc_topology_init - found
-- hwloc version:
-- Found HWLOC: /usr/lib/arm-linux-gnueabihf/libhwloc.so (found suitable version "2.2.0", minimum required is "1.5")
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Looking for C++ include pthread.h
-- Looking for C++ include pthread.h - found
-- Atomic operations found
-- Performing Test PTHREAD_SETAFFINITY
-- Performing Test PTHREAD_SETAFFINITY - Success
-- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.11")
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so - found
-- Checking for GCC x86 inline asm
-- Checking for GCC x86 inline asm - not supported
-- Detected build CPU vendor - ARM
-- Detected build CPU brand - ARMv7 Processor rev 10 (v7l)
-- Detected build CPU family - 7
-- Detected build CPU model - 2
-- Detected build CPU stepping - 10
-- Detected build CPU features - neon
-- Disabling RDTSCP support
-- Checking for 64-bit off_t
-- Checking for 64-bit off_t - present with _FILE_OFFSET_BITS=64
-- Checking for fseeko/ftello
-- Checking for fseeko/ftello - present
-- Checking for SIGUSR1
-- Checking for SIGUSR1 - found
-- Checking for pipe support
-- Checking for system XDR support
-- Checking for system XDR support - present
-- SIMD instructions disabled
-- Performing Test _callconv___vectorcall
-- Performing Test _callconv___vectorcall - Failed
-- Performing Test _callconv___regcall
-- Performing Test _callconv___regcall - Failed
-- Performing Test _callconv_
-- Performing Test _callconv_ - Success
-- pkg-config could not detect fftw3, trying generic detection
-- Looking for fftw_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found
-- Looking for fftw_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found
-- Looking for fftw_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found
-- Looking for fftw_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_vsx in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_vsx in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Using external FFT library - FFTW3
-- Looking for sgemm_
-- Looking for sgemm_ - not found
-- Looking for sgemm_
-- Looking for sgemm_ - found
-- Found BLAS: /usr/lib/arm-linux-gnueabihf/libblas.so
-- Looking for cheev_
-- Looking for cheev_ - not found
-- Looking for cheev_
-- Looking for cheev_ - found
-- A library with LAPACK API found.
-- Checking for dlopen
-- Performing Test HAVE_DLOPEN
-- Performing Test HAVE_DLOPEN - Success
-- Checking for dlopen - found
-- GROMACS only supports plugins in a build that uses shared libraries, which can be disabled for various reasons. BUILD_SHARED_LIBS=on and a toolchain that supports dynamic linking is required. (Hint: GMX_PREFER_STATIC_LIBS and GMX_BUILD_MDRUN_ONLY can influence the default BUILD_SHARED_LIBS, so if you need plugins, reconsider those choices.)
-- Not using dynamic plugins (e.g VMD-supported file formats)
-- Using manually set binary suffix: "_mpi_d.mpich"
-- Using manually set library suffix: "_mpi_d.mpich"
-- Performing Test HAVE_NO_DEPRECATED_COPY
-- Performing Test HAVE_NO_DEPRECATED_COPY - Success
-- Performing Test HAS_NO_STRINGOP_TRUNCATION
-- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success
-- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION
-- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION - Success
-- Performing Test HAS_NO_REDUNDANT_MOVE
-- Performing Test HAS_NO_REDUNDANT_MOVE - Success
-- Performing Test HAS_NO_UNUSED
-- Performing Test HAS_NO_UNUSED - Success
-- Performing Test HAS_NO_UNUSED_PARAMETER
-- Performing Test HAS_NO_UNUSED_PARAMETER - Success
-- Performing Test HAS_NO_MISSING_DECLARATIONS
-- Performing Test HAS_NO_MISSING_DECLARATIONS - Success
-- Performing Test HAS_NO_NULL_CONVERSIONS
-- Performing Test HAS_NO_NULL_CONVERSIONS - Success
-- Performing Test HAS_DECL_IN_SOURCE
-- Performing Test HAS_DECL_IN_SOURCE - Failed
-- Performing Test HAS_NO_CLASS_MEMACCESS
-- Performing Test HAS_NO_CLASS_MEMACCESS - Success
-- Check if the system is big endian
-- Searching 16 bit integer
-- Using unsigned short
-- Check if the system is big endian - little endian
-- Looking for inttypes.h
-- Looking for inttypes.h - found
-- Configuring done
-- Generating done
-- Build files have been written to: /<<PKGBUILDDIR>>/build/mpich-dp
(mkdir -p build/openmpi; cd build/openmpi; CC=/usr/bin/mpicc.openmpi CXX=/usr/bin/mpicxx.openmpi cmake \
/<<PKGBUILDDIR>> -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_VERSION_STRING_OF_FORK="Raspbian-2020.3-1" -DGMX_GIT_VERSION_INFO=OFF -DGMX_SIMD=None -DGMX_MPI=ON -DGMX_X11=OFF -DGMX_DEFAULT_SUFFIX=OFF -DCMAKE_EXE_LINKER_FLAGS="-L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now" -DMPIEXEC="/usr/bin/mpiexec.openmpi" -DGMX_BUILD_MDRUN_ONLY=ON -DGMX_BINARY_SUFFIX="_mpi.openmpi" -DGMX_LIBS_SUFFIX="_mpi.openmpi")
-- The C compiler identification is GNU 9.3.0
-- The CXX compiler identification is GNU 9.3.0
-- Check for working C compiler: /usr/bin/mpicc.openmpi
-- Check for working C compiler: /usr/bin/mpicc.openmpi -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/mpicxx.openmpi
-- Check for working CXX compiler: /usr/bin/mpicxx.openmpi -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Looking for NVIDIA GPUs present in the system
-- Could not detect NVIDIA GPUs
-- No compatible CUDA toolkit found (v5.0+), disabling native GPU acceleration
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- Performing Test CFLAGS_EXCESS_PREC
-- Performing Test CFLAGS_EXCESS_PREC - Success
-- Performing Test CFLAGS_COPT
-- Performing Test CFLAGS_COPT - Success
-- Performing Test CFLAGS_NOINLINE
-- Performing Test CFLAGS_NOINLINE - Success
-- Performing Test CXXFLAGS_EXCESS_PREC
-- Performing Test CXXFLAGS_EXCESS_PREC - Success
-- Performing Test CXXFLAGS_COPT
-- Performing Test CXXFLAGS_COPT - Success
-- Performing Test CXXFLAGS_NOINLINE
-- Performing Test CXXFLAGS_NOINLINE - Success
-- Looking for include file unistd.h
-- Looking for include file unistd.h - found
-- Looking for include file pwd.h
-- Looking for include file pwd.h - found
-- Looking for include file dirent.h
-- Looking for include file dirent.h - found
-- Looking for include file time.h
-- Looking for include file time.h - found
-- Looking for include file sys/time.h
-- Looking for include file sys/time.h - found
-- Looking for include file io.h
-- Looking for include file io.h - not found
-- Looking for include file sched.h
-- Looking for include file sched.h - found
-- Looking for include file xmmintrin.h
-- Looking for include file xmmintrin.h - not found
-- Looking for gettimeofday
-- Looking for gettimeofday - found
-- Looking for sysconf
-- Looking for sysconf - found
-- Looking for nice
-- Looking for nice - found
-- Looking for fsync
-- Looking for fsync - found
-- Looking for _fileno
-- Looking for _fileno - not found
-- Looking for fileno
-- Looking for fileno - found
-- Looking for _commit
-- Looking for _commit - not found
-- Looking for sigaction
-- Looking for sigaction - found
-- Performing Test HAVE_BUILTIN_CLZ
-- Performing Test HAVE_BUILTIN_CLZ - Success
-- Performing Test HAVE_BUILTIN_CLZLL
-- Performing Test HAVE_BUILTIN_CLZLL - Success
-- Looking for clock_gettime in rt
-- Looking for clock_gettime in rt - found
-- Looking for feenableexcept in m
-- Looking for feenableexcept in m - found
-- Looking for fedisableexcept in m
-- Looking for fedisableexcept in m - found
-- Checking for sched.h GNU affinity API
-- Performing Test sched_affinity_compile
-- Performing Test sched_affinity_compile - Success
-- Looking for include file mm_malloc.h
-- Looking for include file mm_malloc.h - not found
-- Looking for include file malloc.h
-- Looking for include file malloc.h - found
-- Checking for _mm_malloc()
-- Checking for _mm_malloc() - not supported
-- Looking for posix_memalign
-- Looking for posix_memalign - found
-- Looking for memalign
-- Looking for memalign - not found
-- Check if the system is big endian
-- Searching 16 bit integer
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of unsigned short
-- Check size of unsigned short - done
-- Using unsigned short
-- Check if the system is big endian - little endian
-- MPI is not compatible with thread-MPI. Disabling thread-MPI.
-- Checking for MPI_IN_PLACE
-- Performing Test MPI_IN_PLACE_COMPILE_OK
-- Performing Test MPI_IN_PLACE_COMPILE_OK - Success
-- Checking for MPI_IN_PLACE - yes
-- Defaulting to building static libraries
-- Looking for HWLOC
-- Looking for hwloc_topology_init
-- Looking for hwloc_topology_init - found
-- hwloc version:
-- Found HWLOC: /usr/lib/arm-linux-gnueabihf/libhwloc.so (found suitable version "2.2.0", minimum required is "1.5")
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
-- Found Threads: TRUE
-- Looking for C++ include pthread.h
-- Looking for C++ include pthread.h - found
-- Atomic operations found
-- Performing Test PTHREAD_SETAFFINITY
-- Performing Test PTHREAD_SETAFFINITY - Success
-- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.11")
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so - found
-- Checking for GCC x86 inline asm
-- Checking for GCC x86 inline asm - not supported
-- Detected build CPU vendor - ARM
-- Detected build CPU brand - ARMv7 Processor rev 10 (v7l)
-- Detected build CPU family - 7
-- Detected build CPU model - 2
-- Detected build CPU stepping - 10
-- Detected build CPU features - neon
-- Disabling RDTSCP support
-- Checking for 64-bit off_t
-- Checking for 64-bit off_t - present with _FILE_OFFSET_BITS=64
-- Checking for fseeko/ftello
-- Checking for fseeko/ftello - present
-- Checking for SIGUSR1
-- Checking for SIGUSR1 - found
-- Checking for pipe support
-- Checking for system XDR support
-- Checking for system XDR support - present
-- SIMD instructions disabled
-- Performing Test _callconv___vectorcall
-- Performing Test _callconv___vectorcall - Failed
-- Performing Test _callconv___regcall
-- Performing Test _callconv___regcall - Failed
-- Performing Test _callconv_
-- Performing Test _callconv_ - Success
-- pkg-config could not detect fftw3f, trying generic detection
-- Looking for fftwf_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Looking for fftwf_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Looking for fftwf_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Looking for fftwf_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Using external FFT library - FFTW3
-- Looking for sgemm_
-- Looking for sgemm_ - not found
-- Looking for sgemm_
-- Looking for sgemm_ - found
-- Found BLAS: /usr/lib/arm-linux-gnueabihf/libblas.so
-- Looking for cheev_
-- Looking for cheev_ - not found
-- Looking for cheev_
-- Looking for cheev_ - found
-- A library with LAPACK API found.
-- Checking for dlopen
-- Performing Test HAVE_DLOPEN
-- Performing Test HAVE_DLOPEN - Success
-- Checking for dlopen - found
-- GROMACS only supports plugins in a build that uses shared libraries, which can be disabled for various reasons. BUILD_SHARED_LIBS=on and a toolchain that supports dynamic linking is required. (Hint: GMX_PREFER_STATIC_LIBS and GMX_BUILD_MDRUN_ONLY can influence the default BUILD_SHARED_LIBS, so if you need plugins, reconsider those choices.)
-- Not using dynamic plugins (e.g VMD-supported file formats)
-- Using manually set binary suffix: "_mpi.openmpi"
-- Using manually set library suffix: "_mpi.openmpi"
-- Performing Test HAVE_NO_DEPRECATED_COPY
-- Performing Test HAVE_NO_DEPRECATED_COPY - Success
-- Performing Test HAS_NO_STRINGOP_TRUNCATION
-- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success
-- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION
-- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION - Success
-- Performing Test HAS_NO_REDUNDANT_MOVE
-- Performing Test HAS_NO_REDUNDANT_MOVE - Success
-- Performing Test HAS_NO_UNUSED
-- Performing Test HAS_NO_UNUSED - Success
-- Performing Test HAS_NO_UNUSED_PARAMETER
-- Performing Test HAS_NO_UNUSED_PARAMETER - Success
-- Performing Test HAS_NO_MISSING_DECLARATIONS
-- Performing Test HAS_NO_MISSING_DECLARATIONS - Success
-- Performing Test HAS_NO_NULL_CONVERSIONS
-- Performing Test HAS_NO_NULL_CONVERSIONS - Success
-- Performing Test HAS_DECL_IN_SOURCE
-- Performing Test HAS_DECL_IN_SOURCE - Failed
-- Performing Test HAS_NO_CLASS_MEMACCESS
-- Performing Test HAS_NO_CLASS_MEMACCESS - Success
-- Check if the system is big endian
-- Searching 16 bit integer
-- Using unsigned short
-- Check if the system is big endian - little endian
-- Looking for inttypes.h
-- Looking for inttypes.h - found
-- Configuring done
-- Generating done
-- Build files have been written to: /<<PKGBUILDDIR>>/build/openmpi
(mkdir -p build/openmpi-dp; cd build/openmpi-dp; CC=/usr/bin/mpicc.openmpi CXX=/usr/bin/mpicxx.openmpi cmake \
/<<PKGBUILDDIR>> -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_VERSION_STRING_OF_FORK="Raspbian-2020.3-1" -DGMX_GIT_VERSION_INFO=OFF -DGMX_SIMD=None -DGMX_MPI=ON -DGMX_X11=OFF -DGMX_DEFAULT_SUFFIX=OFF -DCMAKE_EXE_LINKER_FLAGS="-L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now" -DMPIEXEC="/usr/bin/mpiexec.openmpi" -DGMX_BUILD_MDRUN_ONLY=ON -DGMX_DOUBLE=ON -DGMX_BINARY_SUFFIX="_mpi_d.openmpi" -DGMX_LIBS_SUFFIX="_mpi_d.openmpi")
-- The C compiler identification is GNU 9.3.0
-- The CXX compiler identification is GNU 9.3.0
-- Check for working C compiler: /usr/bin/mpicc.openmpi
-- Check for working C compiler: /usr/bin/mpicc.openmpi -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/mpicxx.openmpi
-- Check for working CXX compiler: /usr/bin/mpicxx.openmpi -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
CMake Warning at cmake/gmxManageGPU.cmake:53 (message):
GPU acceleration is not available in double precision, disabled!
Call Stack (most recent call first):
CMakeLists.txt:217 (include)
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- Performing Test CFLAGS_EXCESS_PREC
-- Performing Test CFLAGS_EXCESS_PREC - Success
-- Performing Test CFLAGS_COPT
-- Performing Test CFLAGS_COPT - Success
-- Performing Test CFLAGS_NOINLINE
-- Performing Test CFLAGS_NOINLINE - Success
-- Performing Test CXXFLAGS_EXCESS_PREC
-- Performing Test CXXFLAGS_EXCESS_PREC - Success
-- Performing Test CXXFLAGS_COPT
-- Performing Test CXXFLAGS_COPT - Success
-- Performing Test CXXFLAGS_NOINLINE
-- Performing Test CXXFLAGS_NOINLINE - Success
-- Looking for include file unistd.h
-- Looking for include file unistd.h - found
-- Looking for include file pwd.h
-- Looking for include file pwd.h - found
-- Looking for include file dirent.h
-- Looking for include file dirent.h - found
-- Looking for include file time.h
-- Looking for include file time.h - found
-- Looking for include file sys/time.h
-- Looking for include file sys/time.h - found
-- Looking for include file io.h
-- Looking for include file io.h - not found
-- Looking for include file sched.h
-- Looking for include file sched.h - found
-- Looking for include file xmmintrin.h
-- Looking for include file xmmintrin.h - not found
-- Looking for gettimeofday
-- Looking for gettimeofday - found
-- Looking for sysconf
-- Looking for sysconf - found
-- Looking for nice
-- Looking for nice - found
-- Looking for fsync
-- Looking for fsync - found
-- Looking for _fileno
-- Looking for _fileno - not found
-- Looking for fileno
-- Looking for fileno - found
-- Looking for _commit
-- Looking for _commit - not found
-- Looking for sigaction
-- Looking for sigaction - found
-- Performing Test HAVE_BUILTIN_CLZ
-- Performing Test HAVE_BUILTIN_CLZ - Success
-- Performing Test HAVE_BUILTIN_CLZLL
-- Performing Test HAVE_BUILTIN_CLZLL - Success
-- Looking for clock_gettime in rt
-- Looking for clock_gettime in rt - found
-- Looking for feenableexcept in m
-- Looking for feenableexcept in m - found
-- Looking for fedisableexcept in m
-- Looking for fedisableexcept in m - found
-- Checking for sched.h GNU affinity API
-- Performing Test sched_affinity_compile
-- Performing Test sched_affinity_compile - Success
-- Looking for include file mm_malloc.h
-- Looking for include file mm_malloc.h - not found
-- Looking for include file malloc.h
-- Looking for include file malloc.h - found
-- Checking for _mm_malloc()
-- Checking for _mm_malloc() - not supported
-- Looking for posix_memalign
-- Looking for posix_memalign - found
-- Looking for memalign
-- Looking for memalign - not found
-- Check if the system is big endian
-- Searching 16 bit integer
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of unsigned short
-- Check size of unsigned short - done
-- Using unsigned short
-- Check if the system is big endian - little endian
-- MPI is not compatible with thread-MPI. Disabling thread-MPI.
-- Checking for MPI_IN_PLACE
-- Performing Test MPI_IN_PLACE_COMPILE_OK
-- Performing Test MPI_IN_PLACE_COMPILE_OK - Success
-- Checking for MPI_IN_PLACE - yes
-- Defaulting to building static libraries
-- Looking for HWLOC
-- Looking for hwloc_topology_init
-- Looking for hwloc_topology_init - found
-- hwloc version:
-- Found HWLOC: /usr/lib/arm-linux-gnueabihf/libhwloc.so (found suitable version "2.2.0", minimum required is "1.5")
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
-- Found Threads: TRUE
-- Looking for C++ include pthread.h
-- Looking for C++ include pthread.h - found
-- Atomic operations found
-- Performing Test PTHREAD_SETAFFINITY
-- Performing Test PTHREAD_SETAFFINITY - Success
-- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.11")
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so - found
-- Checking for GCC x86 inline asm
-- Checking for GCC x86 inline asm - not supported
-- Detected build CPU vendor - ARM
-- Detected build CPU brand - ARMv7 Processor rev 10 (v7l)
-- Detected build CPU family - 7
-- Detected build CPU model - 2
-- Detected build CPU stepping - 10
-- Detected build CPU features - neon
-- Disabling RDTSCP support
-- Checking for 64-bit off_t
-- Checking for 64-bit off_t - present with _FILE_OFFSET_BITS=64
-- Checking for fseeko/ftello
-- Checking for fseeko/ftello - present
-- Checking for SIGUSR1
-- Checking for SIGUSR1 - found
-- Checking for pipe support
-- Checking for system XDR support
-- Checking for system XDR support - present
-- SIMD instructions disabled
-- Performing Test _callconv___vectorcall
-- Performing Test _callconv___vectorcall - Failed
-- Performing Test _callconv___regcall
-- Performing Test _callconv___regcall - Failed
-- Performing Test _callconv_
-- Performing Test _callconv_ - Success
-- pkg-config could not detect fftw3, trying generic detection
-- Looking for fftw_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found
-- Looking for fftw_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found
-- Looking for fftw_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found
-- Looking for fftw_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_vsx in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_vsx in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Using external FFT library - FFTW3
-- Looking for sgemm_
-- Looking for sgemm_ - not found
-- Looking for sgemm_
-- Looking for sgemm_ - found
-- Found BLAS: /usr/lib/arm-linux-gnueabihf/libblas.so
-- Looking for cheev_
-- Looking for cheev_ - not found
-- Looking for cheev_
-- Looking for cheev_ - found
-- A library with LAPACK API found.
-- Checking for dlopen
-- Performing Test HAVE_DLOPEN
-- Performing Test HAVE_DLOPEN - Success
-- Checking for dlopen - found
-- GROMACS only supports plugins in a build that uses shared libraries, which can be disabled for various reasons. BUILD_SHARED_LIBS=on and a toolchain that supports dynamic linking is required. (Hint: GMX_PREFER_STATIC_LIBS and GMX_BUILD_MDRUN_ONLY can influence the default BUILD_SHARED_LIBS, so if you need plugins, reconsider those choices.)
-- Not using dynamic plugins (e.g VMD-supported file formats)
-- Using manually set binary suffix: "_mpi_d.openmpi"
-- Using manually set library suffix: "_mpi_d.openmpi"
-- Performing Test HAVE_NO_DEPRECATED_COPY
-- Performing Test HAVE_NO_DEPRECATED_COPY - Success
-- Performing Test HAS_NO_STRINGOP_TRUNCATION
-- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success
-- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION
-- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION - Success
-- Performing Test HAS_NO_REDUNDANT_MOVE
-- Performing Test HAS_NO_REDUNDANT_MOVE - Success
-- Performing Test HAS_NO_UNUSED
-- Performing Test HAS_NO_UNUSED - Success
-- Performing Test HAS_NO_UNUSED_PARAMETER
-- Performing Test HAS_NO_UNUSED_PARAMETER - Success
-- Performing Test HAS_NO_MISSING_DECLARATIONS
-- Performing Test HAS_NO_MISSING_DECLARATIONS - Success
-- Performing Test HAS_NO_NULL_CONVERSIONS
-- Performing Test HAS_NO_NULL_CONVERSIONS - Success
-- Performing Test HAS_DECL_IN_SOURCE
-- Performing Test HAS_DECL_IN_SOURCE - Failed
-- Performing Test HAS_NO_CLASS_MEMACCESS
-- Performing Test HAS_NO_CLASS_MEMACCESS - Success
-- Check if the system is big endian
-- Searching 16 bit integer
-- Using unsigned short
-- Check if the system is big endian - little endian
-- Looking for inttypes.h
-- Looking for inttypes.h - found
-- Configuring done
-- Generating done
-- Build files have been written to: /<<PKGBUILDDIR>>/build/openmpi-dp
touch configure-stamp
dh_testdir
/usr/bin/make -j4 -C build/basic
make[1]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/cmake -S/<<PKGBUILDDIR>> -B/<<PKGBUILDDIR>>/build/basic --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/build/basic/CMakeFiles /<<PKGBUILDDIR>>/build/basic/CMakeFiles/progress.marks
/usr/bin/make -f CMakeFiles/Makefile2 all
make[2]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend
/usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend
/usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend
/usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/selection /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake --color=
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/CMakeFiles/release-version-info.dir/DependInfo.cmake --color=
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs /<<PKGBUILDDIR>>/build/basic/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -std=c++14 -o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -c /<<PKGBUILDDIR>>/src/external/lmfit/lmmin.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/tmpi_malloc.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/atomic.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/lock.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/pthreads.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/system_error.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/system_error.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/bwt.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/alltoall.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/coder.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/p2p_protocol.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -std=c++14 -o CMakeFiles/scanner.dir/scanner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/scanner.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/dict.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/barrier.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/fixpoint.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/p2p_send_recv.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/huffman.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/bcast.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/p2p_wait.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/collective.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/profile.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/profile.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/comm.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/comm.cpp
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/linearalgebra /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/linearalgebra /<<PKGBUILDDIR>>/build/basic/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake --color=
Scanning dependencies of target linearalgebra
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/eigensolver.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/reduce.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/huffmem.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/gmx_arpack.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/event.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/event.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce_fast.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/reduce_fast.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/gather.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/gather.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/lz77.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scatter.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/scatter.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/merge_sort.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/group.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/mtf.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/tmpi_init.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/rle.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/tng_compress.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/topology.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/list.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/type.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/vals16.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/warnmalloc.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/widemuldiv.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/xtc2.c
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/modularsimulator /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/checkpointhelper.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/matrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/matrix.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/scan.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/numa_malloc.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/once.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/nrjac.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/nrjac.cpp
/usr/bin/make -f src/gromacs/fileio/CMakeFiles/vmddlopen.dir/build.make src/gromacs/fileio/CMakeFiles/vmddlopen.dir/depend
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/fileio /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/CMakeFiles/vmddlopen.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio && /usr/bin/c++ -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/vmddlopen.dir/__/__/external/vmd_molfile/vmddlopen.cpp.o -c /<<PKGBUILDDIR>>/src/external/vmd_molfile/vmddlopen.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/compositesimulatorelement.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/sparsematrix.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/xtc3.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/constraintelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/constraintelement.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/nonbonded_bench.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/lib/tng_io.c
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/buttons.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/buttons.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/domdechelper.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/domdechelper.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/dialogs.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/dialogs.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/energyelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/energyelement.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/fgrid.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/fgrid.cpp
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[ 4%] Built target mdrun_objlib
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/forceelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/forceelement.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/filter.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/filter.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/freeenergyperturbationelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/freeenergyperturbationelement.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/logo.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/logo.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/modularsimulator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/manager.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/manager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/parrinellorahmanbarostat.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/molps.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/molps.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/pmeloadbalancehelper.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/nleg.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/nleg.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/propagator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/propagator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/nmol.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/nmol.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/popup.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/popup.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/pulldown.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/pulldown.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/view.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/view.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/shellfcelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/shellfcelement.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/x11.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/x11.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/xdlg.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xdlg.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/signallers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/signallers.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/xdlghi.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xdlghi.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/lib/md5.c
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/topologyholder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/topologyholder.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/xdlgitem.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xdlgitem.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/trajectoryelement.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/xmb.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xmb.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/xutil.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xutil.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/vrescalethermostat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/vrescalethermostat.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/<<PKGBUILDDIR>>/build/basic/VersionInfo.cmake -D VERSION_CMAKEIN=/<<PKGBUILDDIR>>/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI= -D GMX_RELEASE_HASH= -D GMX_SOURCE_HASH= -P /<<PKGBUILDDIR>>/cmake/gmxConfigureVersionInfo.cmake
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs /<<PKGBUILDDIR>>/build/basic/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/alignedallocator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/any.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/any.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/basenetwork.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/baseversion.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/binaryinformation.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/compare.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/compare.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/coolstuff.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/cstringutil.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/datafilefinder.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/directoryenumerator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/errorcodes.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/errorformat.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/exceptions.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/fatalerror.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/fileredirector.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/filestream.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/filestream.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_prune.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_prune.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm_geometry.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm_setup.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairlistparams.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlistparams.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/gausstransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/gausstransform.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/invertmatrix.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/units.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/units.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/utilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/utilities.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/veccompare.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/veccompare.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/vecdump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/vecdump.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/df_history.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/group.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/iforceprovider.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -Wno-class-memaccess -o CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/inputrec.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/md_enums.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/observableshistory.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpformat.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:40:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:40:
/usr/include/c++/9/bits/stl_vector.h: In function 'void init_gtc_state(t_state*, int, int, int)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helptopic.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpwritercontext.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/rstparser.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/boxutilities.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/mshift.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc_simd.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcenums.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/rmpbc.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/random/seed.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/seed.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tabulatednormaldistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/forcetable.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp: In constructor 'gmx::CubicSplineTable::CubicSplineTable(std::initializer_list<gmx::NumericalSplineTableInput>, const std::pair<float, float>&, real)':
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp:383:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
383 | CubicSplineTable::CubicSplineTable(std::initializer_list<NumericalSplineTableInput> numericalInputList,
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp:383:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp: In constructor 'gmx::QuadraticSplineTable::QuadraticSplineTable(std::initializer_list<gmx::NumericalSplineTableInput>, const std::pair<float, float>&, real)':
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp:367:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
367 | QuadraticSplineTable::QuadraticSplineTable(std::initializer_list<NumericalSplineTableInput> numericalInputList,
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp:170:99: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
170 | std::vector<double> thirdDerivative(internal::vectorSecondDerivative(derivative, inputSpacing));
| ^
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/cyclecounter.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/wallcycle.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/walltime_accounting.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atomprop.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'real gmx::internal::findSmallestQuotientOfFunctionAndSecondDerivative(gmx::ArrayRef<const double>, double, const std::pair<float, float>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:211:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
211 | real findSmallestQuotientOfFunctionAndSecondDerivative(ArrayRef<const double> function,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'real gmx::internal::findSmallestQuotientOfFunctionAndThirdDerivative(gmx::ArrayRef<const double>, double, const std::pair<float, float>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:291:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
291 | real findSmallestQuotientOfFunctionAndThirdDerivative(ArrayRef<const double> function,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'std::vector<double> gmx::internal::vectorSecondDerivative(gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:310:21: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
310 | std::vector<double> vectorSecondDerivative(ArrayRef<const double> f, double spacing)
| ^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'void gmx::internal::throwUnlessDerivativeIsConsistentWithFunction(gmx::ArrayRef<const double>, gmx::ArrayRef<const double>, double, const std::pair<float, float>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:112:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
112 | void throwUnlessDerivativeIsConsistentWithFunction(ArrayRef<const double> function,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:112:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/atoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atoms.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atomsbuilder.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/block.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/block.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/exclusionblocks.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/forcefieldparameters.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/idef.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/idef.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/ifunc.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/index.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/index.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/invblock.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/invblock.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/mtop_util.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/residuetypes.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/symtab.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/symtab.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/topology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/topology.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/topsort.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/topsort.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/swap/swapcoords.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/essentialdynamics/edsam.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pulling/output.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/output.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pulling/pull.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pulling/pull_rotation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pull_rotation.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:39:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_pull_coord&}; _Tp = pull_coord_work_t; _Alloc = std::allocator<pull_coord_work_t>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pull_coord_work_t>::iterator' {aka '__gnu_cxx::__normal_iterator<pull_coord_work_t*, std::vector<pull_coord_work_t> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_pull_group&, gmx::LocalAtomSet, const bool&}; _Tp = pull_group_work_t; _Alloc = std::allocator<pull_group_work_t>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' {aka '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >'} changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_pull_group&, const gmx::LocalAtomSet&, bool&}; _Tp = pull_group_work_t; _Alloc = std::allocator<pull_group_work_t>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' {aka '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >'} changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In function 'pull_t* init_pull(FILE*, const pull_params_t*, const t_inputrec*, const gmx_mtop_t*, const t_commrec*, gmx::LocalAtomSetManager*, real)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pull_coord_work_t*, std::vector<pull_coord_work_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2280:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' {aka '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >'} changed in GCC 7.1
2280 | }
| ^
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2280:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' {aka '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >'} changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2280:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' {aka '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >'} changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2280:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' {aka '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >'} changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/awh.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/awh.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/gmxlib/network.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:45:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/gmxlib/network.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:45:
/usr/include/c++/9/bits/stl_vector.h: In function 'void allocStatePrevStepPullCom(t_state*, const pull_t*)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/bias.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/biasparams.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biasparams.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp: In member function 'void gmx::Bias::updateForceCorrelationGrid(gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:386:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
386 | void Bias::updateForceCorrelationGrid(gmx::ArrayRef<const double> probWeightNeighbor, double t)
| ^~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:406:45: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
406 | state_.calcUmbrellaForceAndPotential(dimParams_, grid_, indexNeighbor, forceFromNeighbor);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:70:
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationgrid.h:104:37: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
104 | tensors_[pointIndex].addData(weight, data, blockLengthMeasure == BlockLengthMeasure::Weight, t);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/biasparams.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/awh/biasparams.cpp:47:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp: In member function 'gmx::ArrayRef<const double> gmx::Bias::calcForceAndUpdateBias(const double*, double*, double*, const t_commrec*, const gmx_multisim_t*, double, int64_t, int64_t, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:144:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
144 | updateForceCorrelationGrid(probWeightNeighbor, t);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
162 | state_.calcConvolvedForce(dimParams_, grid_, probWeightNeighbor, tempForce_, biasForce_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:172:57: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
172 | potential = state_.calcUmbrellaForceAndPotential(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
173 | dimParams_, grid_, coordState.umbrellaGridpoint(), biasForce_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
182 | double newPotential = state_.moveUmbrella(dimParams_, grid_, probWeightNeighbor,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
183 | biasForce_, step, seed, params_.biasIndex);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In constructor 'gmx::BiasParams::BiasParams(const gmx::AwhParams&, const gmx::AwhBiasParams&, const std::vector<gmx::DimParams>&, double, double, gmx::BiasParams::DisableUpdateSkips, int, const std::vector<gmx::GridAxis>&, int)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.cpp:47:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, const double&, const double&}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >'} changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/biassharing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biassharing.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/biasstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::Bias, std::vector<int, std::allocator<int> >&}; _Tp = gmx::BiasCoupledToSystem; _Alloc = std::allocator<gmx::BiasCoupledToSystem>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BiasCoupledToSystem>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BiasCoupledToSystem*, std::vector<gmx::BiasCoupledToSystem> >'} changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In constructor 'gmx::Awh::Awh(FILE*, const t_inputrec&, const t_commrec*, const gmx_multisim_t*, const gmx::AwhParams&, const string&, pull_t*)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BiasCoupledToSystem*, std::vector<gmx::BiasCoupledToSystem> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/biaswriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biaswriter.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/coordstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/coordstate.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In function 'void gmx::{anonymous}::updateTargetDistribution(gmx::ArrayRef<gmx::PointState>, const gmx::BiasParams&)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:292:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::PointState>' changed in GCC 7.1
292 | void updateTargetDistribution(gmx::ArrayRef<PointState> pointState, const BiasParams& params)
| ^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'double gmx::BiasState::calcUmbrellaForceAndPotential(const std::vector<gmx::DimParams>&, const gmx::Grid&, int, gmx::ArrayRef<double>) const':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:416:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
416 | double BiasState::calcUmbrellaForceAndPotential(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::calcConvolvedForce(const std::vector<gmx::DimParams>&, const gmx::Grid&, gmx::ArrayRef<const double>, gmx::ArrayRef<double>, gmx::ArrayRef<double>) const':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:437:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
437 | void BiasState::calcConvolvedForce(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:437:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:437:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:457:38: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
457 | calcUmbrellaForceAndPotential(dimParams, grid, indexNeighbor, forceFromNeighbor);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'double gmx::BiasState::moveUmbrella(const std::vector<gmx::DimParams>&, const gmx::Grid&, gmx::ArrayRef<const double>, gmx::ArrayRef<double>, int64_t, int64_t, int)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:467:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
467 | double BiasState::moveUmbrella(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:467:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:467:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:476:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
476 | coordState_.sampleUmbrellaGridpoint(grid, coordState_.gridpointIndex(), probWeightNeighbor,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
477 | step, seed, indexSeed);
| ~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:476:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:481:42: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
481 | calcUmbrellaForceAndPotential(dimParams, grid, coordState_.umbrellaGridpoint(), newForce);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::sampleProbabilityWeights(const gmx::Grid&, gmx::ArrayRef<const double>)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1233:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1233 | void BiasState::sampleProbabilityWeights(const Grid& grid, gmx::ArrayRef<const double> probWeightNeighbor)
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::sampleCoordAndPmf(const gmx::Grid&, gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1287:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1287 | void BiasState::sampleCoordAndPmf(const Grid& grid, gmx::ArrayRef<const double> probWeightNeighbor, double convolvedBias)
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/coordstate.cpp: In member function 'void gmx::CoordState::sampleUmbrellaGridpoint(const gmx::Grid&, int, gmx::ArrayRef<const double>, int64_t, int64_t, int)':
/<<PKGBUILDDIR>>/src/gromacs/awh/coordstate.cpp:129:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
129 | void CoordState::sampleUmbrellaGridpoint(const Grid& grid,
| ^~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/correlationgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/correlationgrid.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/correlationhistory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/correlationhistory.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::updateFreeEnergyAndAddSamplesToHistogram(const std::vector<gmx::DimParams>&, const gmx::Grid&, const gmx::BiasParams&, const t_commrec*, const gmx_multisim_t*, double, int64_t, FILE*, std::vector<int>*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
1072 | double newHistogramSize = histogramSize_.newHistogramSize(params, t, detectedCovering, points_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1073 | weightSumCovering_, fplog);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/correlationtensor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/grid.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/histogramsize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp: In member function 'void gmx::CorrelationTensor::addData(double, gmx::ArrayRef<const double>, bool, double)':
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp:229:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
229 | void CorrelationTensor::addData(double weight, gmx::ArrayRef<const double> data, bool blockLengthInWeight, double t)
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp:229:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp:47:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {int&, double}; _Tp = gmx::CorrelationBlockData; _Alloc = std::allocator<gmx::CorrelationBlockData>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::CorrelationBlockData>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::CorrelationBlockData*, std::vector<gmx::CorrelationBlockData> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In constructor 'gmx::CorrelationTensor::CorrelationTensor(int, int, double)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::CorrelationBlockData*, std::vector<gmx::CorrelationBlockData> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/pointstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/pointstate.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp: In member function 'double gmx::HistogramSize::newHistogramSizeInitialStage(const gmx::BiasParams&, double, bool, gmx::ArrayRef<double>, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp:77:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
77 | double HistogramSize::newHistogramSizeInitialStage(const BiasParams& params,
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp: In member function 'double gmx::HistogramSize::newHistogramSize(const gmx::BiasParams&, double, bool, const std::vector<gmx::PointState>&, gmx::ArrayRef<double>, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp:209:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
209 | double HistogramSize::newHistogramSize(const BiasParams& params,
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp:242:56: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
242 | newHistogramSize = newHistogramSizeInitialStage(params, t, covered, weightsumCovering, fplog);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp:242:56: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/read_params.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/read_params.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/simd/support.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/support.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/dimparams.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/awh/grid.h:60,
from /<<PKGBUILDDIR>>/src/gromacs/awh/grid.cpp:47:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, double&, double&, double&}; _Tp = gmx::GridAxis; _Alloc = std::allocator<gmx::GridAxis>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::GridAxis>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In constructor 'gmx::Grid::Grid(const std::vector<gmx::DimParams>&, const gmx::AwhDimParams*)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&, const double&, double, int&}; _Tp = gmx::GridAxis; _Alloc = std::allocator<gmx::GridAxis>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::GridAxis>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In function 'void gmx::mapGridToDataGrid(std::vector<int>*, const double* const*, int, const string&, const gmx::Grid&, const string&)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/imd/imd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/imd/imd.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/imd/imdsocket.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/anadih.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/anadih.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/angle_correction.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/angle_correction.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/binsearch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/binsearch.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/cmat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/cmat.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/dens_filter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/dens_filter.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/dlist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/dlist.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/eigio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/eigio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/fitahx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/fitahx.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_anaeig.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_anaeig.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_analyze.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_analyze.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_angle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_angle.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_awh.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_awh.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_bar.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_bar.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_bundle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_bundle.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_chi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_chi.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_cluster.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_cluster.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_clustsize.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_confrms.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_covar.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_current.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_density.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_densmap.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_densorder.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_dielectric.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_dielectric.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_dipoles.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_dipoles.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_disre.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_disre.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_do_dssp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_do_dssp.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_dos.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_dos.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_do_dssp.cpp:47:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_mapping&}; _Tp = t_mapping; _Alloc = std::allocator<t_mapping>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_mapping>::iterator' {aka '__gnu_cxx::__normal_iterator<t_mapping*, std::vector<t_mapping> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_dyecoupl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_dyecoupl.cpp
/usr/include/c++/9/bits/vector.tcc: In function 'int gmx_do_dssp(int, char**)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_mapping*, std::vector<t_mapping> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_wheel.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_wheel.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_xpm2ps.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/hxprops.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/hxprops.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/nrama.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/nrama.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp: In function 'void rainbow_map(gmx_bool, gmx::ArrayRef<t_mapping>)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:1328:13: note: parameter passing for argument of type 'gmx::ArrayRef<t_mapping>' changed in GCC 7.1
1328 | static void rainbow_map(gmx_bool bBlue, gmx::ArrayRef<t_mapping> map)
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp: In function 'void leg_continuous(t_psdata*, real, real, real, const string&, real, char*, gmx::ArrayRef<const t_mapping>, int)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:249:13: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
249 | static void leg_continuous(t_psdata* ps,
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/nsfactor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/nsfactor.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/powerspect.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/powerspect.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp: In function 'void ps_mat(const char*, gmx::ArrayRef<t_matrix>, gmx::ArrayRef<t_matrix>, gmx_bool, gmx_bool, gmx_bool, gmx_bool, gmx_bool, gmx_bool, int, real, real, real, const char*, const char*, int)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:1033:31: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
1033 | leg_continuous(&out, x0 + w / 2, w / 2, DDD, legend, psr->legfontsize, psr->legfont,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1034 | leg_map, mapoffset);
| ~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:1033:31: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:316:19: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
316 | leg_continuous(ps, xx1, x1, y0, label1, fontsize, font, map1, 0);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:316:19: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:317:19: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
317 | leg_continuous(ps, xx2, x2, y0, label2, fontsize, font, map2, 0);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:317:19: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/pp2shift.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/pp2shift.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp: In function 'int gmx_xpm2ps(int, char**)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:1376:20: note: parameter passing for argument of type 'gmx::ArrayRef<t_mapping>' changed in GCC 7.1
1376 | rainbow_map(bBlue, m.map);
| ~~~~~~~~~~~^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:1376:20: note: parameter passing for argument of type 'gmx::ArrayRef<t_mapping>' changed in GCC 7.1
1376 | rainbow_map(bBlue, m.map);
| ~~~~~~~~~~~^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/princ.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/princ.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/sfactor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/sfactor.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/thermochemistry.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/add_par.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/calch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/calch.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/convparm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/convparm.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/editconf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/editconf.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/fflibutil.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_maxwell_velocities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_maxwell_velocities.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_vsite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/genconf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genconf.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/genhydro.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genhydro.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setvelocities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/setvelocities.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/coordinateio/requirements.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/requirements.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/analysismodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysismodule.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/analysissettings.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysissettings.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/cmdlinerunner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/cmdlinerunner.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/angle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/angle.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/convert_trj.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/convert_trj.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/distance.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/distance.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/extract_cluster.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/extract_cluster.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/freevolume.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/pairdist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/pairdist.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysismodule.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.cpp:44:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/rdf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/rdf.cpp
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void gmx::analysismodules::{anonymous}::FreeVolume::initAnalysis(const gmx::TrajectoryAnalysisSettings&, const gmx::TopologyInformation&)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/sasa.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/sasa.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/select.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/select.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/surfacearea.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/trajectory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/trajectory.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/runnercommon.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/runnercommon.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/topologyinformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/topologyinformation.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tools/check.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/check.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tools/convert_tpr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/convert_tpr.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tools/dump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/dump.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qm_orca.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_orca.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qmmm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qmmm.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/resethandler.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/rf_util.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/settle.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/sighandler.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/simulationsignal.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/splitter.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/stat.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/stophandler.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tgroup.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/trajectory_writing.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/update.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/update_constrain_cuda_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/update_constrain_cuda_impl.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update_constrain_cuda_impl.cpp: In member function 'void gmx::UpdateConstrainCuda::integrate(GpuEventSynchronizer*, real, bool, bool, real (*)[3], bool, gmx::ArrayRef<const t_grp_tcstat>, bool, float, const real (*)[3])':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update_constrain_cuda_impl.cpp:70:6: note: parameter passing for argument of type 'gmx::ArrayRef<const t_grp_tcstat>' changed in GCC 7.1
70 | void UpdateConstrainCuda::integrate(GpuEventSynchronizer* /* fReadyOnDevice */,
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroups.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/vcm.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/long_range_correction.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/long_range_correction.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_gather.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_gather.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_grid.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_load_balancing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_only.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_pp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_pp.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/forcerec.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp:47:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const pme_setup_t&}; _Tp = pme_setup_t; _Alloc = std::allocator<pme_setup_t>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pme_setup_t>::iterator' {aka '__gnu_cxx::__normal_iterator<pme_setup_t*, std::vector<pme_setup_t> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/forcerec.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp:47:
/usr/include/c++/9/bits/stl_vector.h: In function 'void pme_load_balance(pme_load_balancing_t*, t_commrec*, FILE*, FILE*, const gmx::MDLogger&, const t_inputrec&, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<float> >, double, interaction_const_t*, nonbonded_verlet_t*, gmx_pme_t**, int64_t)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pme_setup_t*, std::vector<pme_setup_t> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_redistribute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_redistribute.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_solve.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_solve.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_spline_work.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_spline_work.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_spread.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_spread.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_gpu_program.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_pp_comm_gpu_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_coordinate_receiver_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_coordinate_receiver_gpu_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_force_sender_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_force_sender_gpu_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_gpu_program_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fft/calcgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/calcgrid.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fft/fft.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/fft.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fft/fft5d.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/fft5d.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fft/parallel_3dfft.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/parallel_3dfft.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fft/fft_fftw3.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/fft_fftw3.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/clfftinitializer.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gpu_utils/hostallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/gpu_utils.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gpu_utils/gpu_testutils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/gpu_testutils.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/cpuinfo.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/cpuinfo.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/detecthardware.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/detecthardware.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/gpu_hw_info.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/gpu_hw_info.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/hardwaretopology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/hardwaretopology.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/printhardware.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/printhardware.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/identifyavx512fmaunits.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/identifyavx512fmaunits.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/legacymdrunoptions.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/legacysimulator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/md.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/mdmodules.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/mdmodules.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/replicaexchange.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp: In member function 'void gmx::LegacySimulator::do_md()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1293:34: note: parameter passing for argument of type 'gmx::ArrayRef<const t_grp_tcstat>' changed in GCC 7.1
1293 | integrator->integrate(stateGpu->getForcesReadyOnDeviceEvent(
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1294 | AtomLocality::Local, runScheduleWork->stepWork.useGpuFBufferOps),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1295 | ir->delta_t, true, bCalcVir, shake_vir, doTemperatureScaling,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1296 | ekind->tcstat, doParrinelloRahman, ir->nstpcouple * ir->delta_t, M);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/rerun.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/shellfc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/simulationcontext.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/handlerestart.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/logging.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/multisim.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/printtime.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/threadaffinity.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/abstractoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/abstractoption.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/abstractsection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/abstractsection.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/basicoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/behaviorcollection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/behaviorcollection.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/filenameoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/filenameoption.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/filenameoptionmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/filenameoptionmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/options.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/options.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/optionsassigner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/optionsassigner.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/optionsection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/optionsection.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/optionsvisitor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/optionsvisitor.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/timeunitmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/timeunitmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/treesupport.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/treesupport.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/restraint/manager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/restraint/manager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/restraint/restraintmdmodule.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual void gmx::DoubleOptionStorage::processSetValues(gmx::OptionStorageTemplate<double>::ValueList*)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/decidegpuusage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/decidegpuusage.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/decidesimulationworkload.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/decidesimulationworkload.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/9/bits/stl_vector.h: In member function 'void gmx::OptionStorageTemplate<T>::addValue(const T&) [with T = double]':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreNull<T>::append(const T&) [with T = double]':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreVector<T>::append(const T&) [with T = double]':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<long long int, std::allocator<long long int> >::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/9/bits/stl_vector.h: In member function 'void gmx::OptionStorageTemplate<T>::addValue(const T&) [with T = long long int]':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreVector<T>::append(const T&) [with T = long long int]':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreNull<T>::append(const T&) [with T = long long int]':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/findallgputasks.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/findallgputasks.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/reportgpuusage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/reportgpuusage.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/resourcedivision.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/resourcedivision.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/taskassignment.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/taskassignment.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/usergpuids.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/usergpuids.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectory/energyframe.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectory/trajectoryframe.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mimic/communicator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mimic/utilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mimic/utilities.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o -c /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/baseversion-gen.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/checkpoint.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/confio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/confio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/enxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/enxio.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.h:39,
from /<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.cpp:37:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void gmx::MimicCommunicator::sendForces(gmx::ArrayRef<gmx::BasicVector<float> >, int)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/espio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/espio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/filetypes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/filetypes.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/g96io.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/gmx_internal_xdr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmx_internal_xdr.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/gmxfio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/gmxfio_xdr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio_xdr.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.cpp:39:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {}; _Tp = gmx_file_position_t; _Alloc = std::allocator<gmx_file_position_t>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx_file_position_t>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx_file_position_t*, std::vector<gmx_file_position_t> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In function 'std::vector<gmx_file_position_t> gmx_fio_get_output_file_positions()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx_file_position_t*, std::vector<gmx_file_position_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/groio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/groio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/libxdrf.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/matio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/md5.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/md5.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/mrcdensitymap.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mrcdensitymap.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/mrcdensitymapheader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mrcdensitymapheader.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/mrcserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mrcserializer.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mtxio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/oenv.cpp
/<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp: In function 't_matelmt searchcmap(gmx::ArrayRef<const t_mapping>, t_xpmelmt)':
/<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp:114:11: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
114 | t_matelmt searchcmap(ArrayRef<const t_mapping> map, t_xpmelmt c)
| ^~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/pdbio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/pdbio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/readinp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/readinp.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/timecontrol.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/timecontrol.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/tngio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tngio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tpxio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/trrio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/trrio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/trxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/trxio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/vmdio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/vmdio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/warninp.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/writeps.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/xdrd.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/writeps.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/writeps.cpp:39:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_rgb}; _Tp = t_rgb; _Alloc = std::allocator<t_rgb>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_rgb>::iterator' {aka '__gnu_cxx::__normal_iterator<t_rgb*, std::vector<t_rgb> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_rgb>::iterator' {aka '__gnu_cxx::__normal_iterator<t_rgb*, std::vector<t_rgb> >'} changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/xtcio.cpp
/usr/include/c++/9/bits/vector.tcc: In function 'gmx::index search_col(t_psdata*, real, real, real)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_rgb*, std::vector<t_rgb> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/xvgr.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/centerofmass.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/centerofmass.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/compiler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/compiler.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/evaluate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/evaluate.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/indexutil.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/mempool.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/mempool.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/params.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/params.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/parsetree.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/poscalc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/poscalc.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/position.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/position.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/scanner_internal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/scanner_internal.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selection.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selectioncollection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selectioncollection.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selectionoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selectionoption.cpp
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CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o /usr/lib/arm-linux-gnueabihf/libhwloc.so -ldl -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so -lpthread -lm /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lpthread -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgromacs.so.5.0.0 ../../lib/libgromacs.so.5 ../../lib/libgromacs.so
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/api/cpp /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/api/cpp /<<PKGBUILDDIR>>/build/basic/src/api/cpp/CMakeFiles/gmxapi.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs /<<PKGBUILDDIR>>/build/basic/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/share/template /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/share/template /<<PKGBUILDDIR>>/build/basic/share/template/CMakeFiles/template.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmx.dir/gmx.cpp.o -c /<<PKGBUILDDIR>>/src/programs/gmx.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmx.dir/legacymodules.cpp.o -c /<<PKGBUILDDIR>>/src/programs/legacymodules.cpp
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cd /<<PKGBUILDDIR>>/build/basic/share/template && /usr/bin/c++ -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -std=c++14 -o CMakeFiles/template.dir/template.cpp.o -c /<<PKGBUILDDIR>>/share/template/template.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/context.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/context.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/exceptions.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/exceptions.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/gmxapi.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/gmxapi.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/md.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/md.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmx.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gmx.dir/gmx.cpp.o CMakeFiles/gmx.dir/legacymodules.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o CMakeFiles/view_objlib.dir/view/3dview.cpp.o CMakeFiles/view_objlib.dir/view/buttons.cpp.o CMakeFiles/view_objlib.dir/view/dialogs.cpp.o CMakeFiles/view_objlib.dir/view/fgrid.cpp.o CMakeFiles/view_objlib.dir/view/filter.cpp.o CMakeFiles/view_objlib.dir/view/logo.cpp.o CMakeFiles/view_objlib.dir/view/manager.cpp.o CMakeFiles/view_objlib.dir/view/molps.cpp.o CMakeFiles/view_objlib.dir/view/nleg.cpp.o CMakeFiles/view_objlib.dir/view/nmol.cpp.o CMakeFiles/view_objlib.dir/view/popup.cpp.o CMakeFiles/view_objlib.dir/view/pulldown.cpp.o CMakeFiles/view_objlib.dir/view/view.cpp.o CMakeFiles/view_objlib.dir/view/x11.cpp.o CMakeFiles/view_objlib.dir/view/xdlg.cpp.o CMakeFiles/view_objlib.dir/view/xdlghi.cpp.o CMakeFiles/view_objlib.dir/view/xdlgitem.cpp.o CMakeFiles/view_objlib.dir/view/xmb.cpp.o CMakeFiles/view_objlib.dir/view/xutil.cpp.o -o ../../bin/gmx ../../lib/libgromacs.so.5.0.0 /usr/lib/arm-linux-gnueabihf/libX11.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so
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cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/mdmodule.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/mdmodule.cpp
cd /<<PKGBUILDDIR>>/build/basic/share/template && /usr/bin/cmake -E cmake_link_script CMakeFiles/template.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/template.dir/template.cpp.o -o ../../bin/template ../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so
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cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/mdsignals.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/mdsignals.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/session.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/session.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/status.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/status.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/system.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/system.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/version.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/version.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/workflow.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/workflow.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/tpr.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tpr.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgmxapi.so.0 -o ../../../lib/libgmxapi.so.0.1.0 CMakeFiles/gmxapi.dir/context.cpp.o CMakeFiles/gmxapi.dir/exceptions.cpp.o CMakeFiles/gmxapi.dir/gmxapi.cpp.o CMakeFiles/gmxapi.dir/md.cpp.o CMakeFiles/gmxapi.dir/mdmodule.cpp.o CMakeFiles/gmxapi.dir/mdsignals.cpp.o CMakeFiles/gmxapi.dir/session.cpp.o CMakeFiles/gmxapi.dir/status.cpp.o CMakeFiles/gmxapi.dir/system.cpp.o CMakeFiles/gmxapi.dir/version.cpp.o CMakeFiles/gmxapi.dir/workflow.cpp.o CMakeFiles/gmxapi.dir/tpr.cpp.o ../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libgmxapi.so.0.1.0 ../../../lib/libgmxapi.so.0 ../../../lib/libgmxapi.so
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/bwlzh.c
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/bwt.c
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/tmpi_malloc.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/atomic.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/lock.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/pthreads.cpp
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make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -std=c++14 -o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -c /<<PKGBUILDDIR>>/src/external/lmfit/lmmin.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/system_error.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/system_error.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/coder.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/alltoall.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/p2p_protocol.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/dict.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/fixpoint.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/huffman.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/barrier.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/p2p_send_recv.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 0%] Built target lmfit_objlib
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/huffmem.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/bcast.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/p2p_wait.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/lz77.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -std=c++14 -o CMakeFiles/scanner.dir/scanner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/scanner.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/collective.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/profile.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/profile.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/comm.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/comm.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/merge_sort.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/mtf.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/reduce.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/rle.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/event.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/event.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/tng_compress.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce_fast.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/reduce_fast.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/gather.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/gather.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scatter.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/scatter.cpp
/usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/linearalgebra /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/linearalgebra /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake --color=
Scanning dependencies of target linearalgebra
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
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make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/eigensolver.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/group.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/tmpi_init.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/gmx_arpack.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/topology.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/list.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/type.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/vals16.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/warnmalloc.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/widemuldiv.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/xtc2.c
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 0%] Built target scanner
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/xtc3.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/scan.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/numa_malloc.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/once.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 3%] Built target thread_mpi
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/lib/tng_io.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/lib/md5.c
/usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/modularsimulator /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake --color=
Scanning dependencies of target modularsimulator
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/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/checkpointhelper.cpp: In member function 'void gmx::CheckpointHelper::writeCheckpoint(gmx::Step, gmx::Time)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/checkpointhelper.cpp:129:37: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
129 | mdoutf_write_to_trajectory_files(fplog_, cr_, trajectoryElement_->outf_, MDOF_CPT,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
130 | globalNumAtoms_, step, time, localStateInstance_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
131 | state_global_, observablesHistory_, ArrayRef<RVec>());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/domdechelper.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/domdechelper.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/energyelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/energyelement.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/manager.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/manager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/molps.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/molps.cpp
/<<PKGBUILDDIR>>/src/programs/view/manager.cpp: In function 'bool ManCallBack(t_x11*, XEvent*, Window, void*)':
/<<PKGBUILDDIR>>/src/programs/view/manager.cpp:366:46: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
366 | put_atoms_in_compact_unitcell(man->molw->ePBC, ecenterDEF, man->box, atomsArrayRef);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/programs/view/manager.cpp:366:46: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/forceelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/forceelement.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/nleg.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/nleg.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/energyelement.cpp: In member function 'void gmx::EnergyElement::doStep(gmx::Time, bool, bool)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/energyelement.cpp:239:17: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
239 | sum_dhdl(enerd_, freeEnergyPerturbationElement_->constLambdaView(), *inputrec_->fepvals);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/nmol.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/nmol.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/freeenergyperturbationelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/freeenergyperturbationelement.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/forceelement.cpp: In member function 'void gmx::ForceElement::run(gmx::Step, gmx::Time, unsigned int)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/forceelement.cpp:159:13: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
159 | do_force(fplog_, cr_, ms, inputrec_, awh, enforcedRotation_, imdSession_, pull_work_, step,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
160 | nrnb_, wcycle_, localTopology_, box, x, hist, forces, force_vir, mdAtoms_->mdatoms(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
161 | energyElement_->enerdata(), fcd_, lambda, graph, fr_, runScheduleWork_, vsite_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
162 | energyElement_->muTot(), time, ed, static_cast<int>(flags), ddBalanceRegionHandler_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/popup.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/popup.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/modularsimulator.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/freeenergyperturbationelement.cpp: In constructor 'gmx::FreeEnergyPerturbationElement::FreeEnergyPerturbationElement(FILE*, const t_inputrec*, gmx::MDAtoms*)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/freeenergyperturbationelement.cpp:67:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
67 | initialize_lambdas(fplog_, *inputrec_, true, ¤tFEPState_, lambda_, lambda0_.data());
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/freeenergyperturbationelement.cpp: In member function 'void gmx::FreeEnergyPerturbationElement::updateLambdas(gmx::Step)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/freeenergyperturbationelement.cpp:85:27: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
85 | setCurrentLambdasLocal(step, inputrec_->fepvals, lambda0_.data(), lambda_, currentFEPState_);
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/pulldown.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/pulldown.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/parrinellorahmanbarostat.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/view.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/view.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/parrinellorahmanbarostat.cpp: In constructor 'gmx::ParrinelloRahmanBarostat::ParrinelloRahmanBarostat(int, int, real, gmx::Step, gmx::ArrayRef<double [3]>, gmx::PropagatorCallbackPtr, gmx::StatePropagatorData*, gmx::EnergyElement*, FILE*, const t_inputrec*, const gmx::MDAtoms*, const t_state*, t_commrec*, bool)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/parrinellorahmanbarostat.cpp:62:1: note: parameter passing for argument of type 'gmx::ArrayRef<double [3]>' changed in GCC 7.1
62 | ParrinelloRahmanBarostat::ParrinelloRahmanBarostat(int nstpcouple,
| ^~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/x11.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/x11.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/pmeloadbalancehelper.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/xdlg.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xdlg.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 6%] Built target tng_io_obj
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/xdlghi.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xdlghi.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/pmeloadbalancehelper.cpp: In member function 'void gmx::PmeLoadBalanceHelper::run(gmx::Step, gmx::Time)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/pmeloadbalancehelper.cpp:107:19: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
107 | pme_loadbal_do(pme_loadbal_, cr_, (isVerbose_ && MASTER(cr_)) ? stderr : nullptr, fplog_,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
108 | mdlog_, *inputrec_, fr_, statePropagatorData_->constBox(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
109 | statePropagatorData_->constPositionsView().paddedArrayRef(), wcycle_, step,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
110 | step - inputrec_->init_step, &bPMETunePrinting_, false);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/xdlgitem.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xdlgitem.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/propagator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/propagator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/xmb.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xmb.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/shellfcelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/shellfcelement.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/xutil.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xutil.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 9%] Built target view_objlib
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/signallers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/signallers.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/shellfcelement.cpp: In member function 'void gmx::ShellFCElement::run(gmx::Step, gmx::Time, bool, unsigned int)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/shellfcelement.cpp:185:24: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
185 | relax_shell_flexcon(fplog_, cr_, ms, isVerbose_, enforcedRotation_, step, inputrec_, imdSession_,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
186 | pull_work_, isNSStep, static_cast<int>(flags), localTopology_, constr_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
187 | energyElement_->enerdata(), fcd_, statePropagatorData_->localNumAtoms(), x,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
188 | v, box, lambda, hist, forces, force_vir, mdAtoms_->mdatoms(), nrnb_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
189 | wcycle_, graph, shellfc_, fr_, runScheduleWork_, time,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
190 | energyElement_->muTot(), vsite_, ddBalanceRegionHandler_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/topologyholder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/topologyholder.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp: In function 'virtual void gmx::StatePropagatorData::trajectoryWriterTeardown(gmx_mdoutf*)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:464:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
464 | dd_collect_vec(cr_->dd, localStateBackup_.get(), localStateBackup_->x, globalXRef);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:466:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
466 | dd_collect_vec(cr_->dd, localStateBackup_.get(), localStateBackup_->v, globalVRef);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/trajectoryelement.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/vrescalethermostat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/vrescalethermostat.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp: In member function 'void gmx::StatePropagatorData::write(gmx_mdoutf_t, gmx::Step, gmx::Time)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:411:37: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
411 | mdoutf_write_to_trajectory_files(fplog_, cr_, outf, static_cast<int>(mdof_flags),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
412 | totalNumAtoms_, currentStep, currentTime,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
413 | localStateBackup_.get(), globalState_, observablesHistory, f_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/stophandler.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/isimulator.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/modularsimulator.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/modularsimulator.cpp:44:
/usr/include/c++/9/bits/unique_ptr.h: In member function 'std::unique_ptr<gmx::ISimulatorElement> gmx::ModularSimulator::buildIntegrator(gmx::SignallerBuilder<gmx::NeighborSearchSignaller>*, gmx::SignallerBuilder<gmx::EnergySignaller>*, gmx::SignallerBuilder<gmx::LoggingSignaller>*, gmx::TrajectoryElementBuilder*, std::vector<gmx::ICheckpointHelperClient*>*, gmx::CheckBondedInteractionsCallbackPtr*, gmx::compat::not_null<gmx::StatePropagatorData*>, gmx::compat::not_null<gmx::EnergyElement*>, gmx::FreeEnergyPerturbationElement*, bool)':
/usr/include/c++/9/bits/unique_ptr.h:857:30: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
857 | { return unique_ptr<_Tp>(new _Tp(std::forward<_Args>(__args)...)); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/unique_ptr.h:857:30: note: parameter passing for argument of type 'gmx::ArrayRef<double [3]>' changed in GCC 7.1
857 | { return unique_ptr<_Tp>(new _Tp(std::forward<_Args>(__args)...)); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/unique_ptr.h:857:30: note: parameter passing for argument of type 'gmx::ArrayRef<double [3]>' changed in GCC 7.1
857 | { return unique_ptr<_Tp>(new _Tp(std::forward<_Args>(__args)...)); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/unique_ptr.h:857:30: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
857 | { return unique_ptr<_Tp>(new _Tp(std::forward<_Args>(__args)...)); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:44:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:44:
/usr/include/c++/9/bits/stl_vector.h: In member function 'void gmx::StatePropagatorData::setLocalState(std::unique_ptr<t_state>)':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/vrescalethermostat.cpp: In constructor 'gmx::VRescaleThermostat::VRescaleThermostat(int, int, bool, int64_t, int, double, const real*, const real*, const real*, gmx::EnergyElement*, gmx::ArrayRef<double>, gmx::PropagatorCallbackPtr, const t_state*, t_commrec*, bool)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/vrescalethermostat.cpp:59:1: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
59 | VRescaleThermostat::VRescaleThermostat(int nstcouple,
| ^~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In function 'void gmx::changePinningPolicy(PinnableVector*, gmx::PinningPolicy) [with PinnableVector = gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >]':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In constructor 'gmx::StatePropagatorData::StatePropagatorData(int, FILE*, const t_commrec*, t_state*, int, int, int, int, bool, gmx::FreeEnergyPerturbationElement*, const gmx::TopologyHolder*, bool, bool, std::string, const t_inputrec*, const t_mdatoms*)':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 10%] Built target modularsimulator
/usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/<<PKGBUILDDIR>>/build/basic-dp/VersionInfo.cmake -D VERSION_CMAKEIN=/<<PKGBUILDDIR>>/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI= -D GMX_RELEASE_HASH= -D GMX_SOURCE_HASH= -P /<<PKGBUILDDIR>>/cmake/gmxConfigureVersionInfo.cmake
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color=
Scanning dependencies of target libgromacs
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make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/alignedallocator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/any.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/any.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/basenetwork.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/baseversion.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/binaryinformation.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/compare.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/compare.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/coolstuff.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/cstringutil.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/datafilefinder.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/directoryenumerator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/errorcodes.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/errorformat.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/exceptions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/fatalerror.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/fileredirector.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/filestream.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/filestream.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/futil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/futil.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/gmxassert.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/gmxassert.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/gmxomp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/gmxomp.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/ikeyvaluetreeerror.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/ikeyvaluetreeerror.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/init.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/init.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/inmemoryserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/inmemoryserializer.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/sysinfo.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/sysinfo.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/textreader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/textreader.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/textwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/textwriter.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/txtdump.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/atomdata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_setup.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_system.cpp
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_setup.cpp: In function 'void Nbnxm::setupAndRunInstance(const gmx::BenchmarkSystem&, const Nbnxm::KernelBenchOptions&, bool)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_setup.cpp:222:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
222 | nbnxn_put_on_grid(nbv.get(), system.box, 0, lowerCorner, upperCorner, nullptr,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
223 | { 0, int(system.coordinates.size()) }, atomDensity, atomInfo,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
224 | system.coordinates, 0, nullptr);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/atomdata.cpp: In function 'void nbnxn_atomdata_add_nbat_fshift_to_fshift(const nbnxn_atomdata_t&, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/atomdata.cpp:1484:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1484 | void nbnxn_atomdata_add_nbat_fshift_to_fshift(const nbnxn_atomdata_t& nbat, gmx::ArrayRef<gmx::RVec> fshift)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_setup.cpp:50:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Nbnxm::KernelBenchOptions&}; _Tp = Nbnxm::KernelBenchOptions; _Alloc = std::allocator<Nbnxm::KernelBenchOptions>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<Nbnxm::KernelBenchOptions>::iterator' {aka '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_setup.cpp:50:
/usr/include/c++/9/bits/stl_vector.h: In function 'void Nbnxm::bench(int, const Nbnxm::KernelBenchOptions&)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/gridset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernel_common.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernel_common.cpp
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp: In member function 'void Nbnxm::Grid::fillCell(Nbnxm::GridSetData*, nbnxn_atomdata_t*, int, int, const int*, gmx::ArrayRef<const gmx::BasicVector<double> >, Nbnxm::BoundingBox*)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:859:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
859 | void Grid::fillCell(GridSetData* gridSetData,
| ^~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp: In function '_ZN5Nbnxm7GridSet9putOnGridEPA3_KdiPS1_S4_PKN3gmx15UpdateGroupsCogENS5_5RangeIiEEdNS5_8ArrayRefIKiEENSB_IKNS5_11BasicVectorIdEEEEiPSC_P16nbnxn_atomdata_t._omp_fn.0':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp:216:36: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
216 | Grid::calcColumnIndices(grid.dimensions(), updateGroupsCog, atomRange, x, ddZone, move, thread,
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
217 | nthread, gridSetData_.cells, gridWork_[thread].numAtomsPerColumn);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp: In member function 'void Nbnxm::Grid::sortColumnsCpuGeometry(Nbnxm::GridSetData*, int, const int*, gmx::ArrayRef<const gmx::BasicVector<double> >, nbnxn_atomdata_t*, gmx::Range<int>, gmx::ArrayRef<int>)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:987:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
987 | void Grid::sortColumnsCpuGeometry(GridSetData* gridSetData,
| ^~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:1027:21: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1027 | fillCell(gridSetData, nbat, atomOffsetCell, atomOffsetCell + numAtomsCell, atinfo, x, nullptr);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp: In member function 'void Nbnxm::Grid::sortColumnsGpuGeometry(Nbnxm::GridSetData*, int, const int*, gmx::ArrayRef<const gmx::BasicVector<double> >, nbnxn_atomdata_t*, gmx::Range<int>, gmx::ArrayRef<int>)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:1050:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1050 | void Grid::sortColumnsGpuGeometry(GridSetData* gridSetData,
| ^~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:1151:29: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1151 | fillCell(gridSetData, nbat, atomOffsetX, atomOffsetX + numAtomsX, atinfo, x,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1152 | bb_work_aligned);
| ~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp: In member function 'void Nbnxm::GridSet::putOnGrid(const real (*)[3], int, const real*, const real*, const gmx::UpdateGroupsCog*, gmx::Range<int>, real, gmx::ArrayRef<const int>, gmx::ArrayRef<const gmx::BasicVector<double> >, int, const int*, nbnxn_atomdata_t*)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp:136:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
136 | void GridSet::putOnGrid(const matrix box,
| ^~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp:223:24: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
223 | grid.setCellIndices(ddZone, cellOffset, &gridSetData_, gridWork_, atomRange, atomInfo.data(), x,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
224 | numAtomsMoved, nbat);
| ~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp: In function '_ZN5Nbnxm4Grid14setCellIndicesEiiPNS_11GridSetDataEN3gmx8ArrayRefINS_8GridWorkEEENS3_5RangeIiEEPKiNS4_IKNS3_11BasicVectorIdEEEEiP16nbnxn_atomdata_t._omp_fn.0':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:1409:39: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1409 | sortColumnsGpuGeometry(gridSetData, ddZone, atinfo, x, nbat, columnRange,
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1410 | gridWork[thread].sortBuffer);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:1404:39: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1404 | sortColumnsCpuGeometry(gridSetData, ddZone, atinfo, x, nbat, columnRange,
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1405 | gridWork[thread].sortBuffer);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp: In static member function 'static void Nbnxm::Grid::calcColumnIndices(const Nbnxm::Grid::Dimensions&, const gmx::UpdateGroupsCog*, gmx::Range<int>, gmx::ArrayRef<const gmx::BasicVector<double> >, int, const int*, int, int, gmx::ArrayRef<int>, gmx::ArrayRef<int>)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:1172:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1172 | void Grid::calcColumnIndices(const Grid::Dimensions& gridDims,
| ^~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kerneldispatch.cpp
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp: In member function 'void Nbnxm::Grid::setCellIndices(int, int, Nbnxm::GridSetData*, gmx::ArrayRef<Nbnxm::GridWork>, gmx::Range<int>, const int*, gmx::ArrayRef<const gmx::BasicVector<double> >, int, nbnxn_atomdata_t*)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:1286:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1286 | void Grid::setCellIndices(int ddZone,
| ^~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_ref.cpp
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/kerneldispatch.cpp: In member function 'void nonbonded_verlet_t::dispatchNonbondedKernel(gmx::InteractionLocality, const interaction_const_t&, const gmx::StepWorkload&, int, const t_forcerec&, gmx_enerdata_t*, t_nrnb*)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/kerneldispatch.cpp:442:33: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
442 | nbnxn_kernel_gpu_ref(
| ~~~~~~~~~~~~~~~~~~~~^
443 | pairlistSet.gpuList(), nbat.get(), &ic, fr.shift_vec, stepWork, clearF,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
444 | nbat->out[0].f, nbat->out[0].fshift.data(), enerd->grpp.ener[egCOULSR].data(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
445 | fr.bBHAM ? enerd->grpp.ener[egBHAMSR].data() : enerd->grpp.ener[egLJSR].data());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_ref_prune.cpp
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp: In function 'void nbnxn_kernel_gpu_ref(const NbnxnPairlistGpu*, const nbnxn_atomdata_t*, const interaction_const_t*, real (*)[3], const gmx::StepWorkload&, int, gmx::ArrayRef<double>, real*, real*, real*)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp:57:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
57 | void nbnxn_kernel_gpu_ref(const NbnxnPairlistGpu* nbl,
| ^~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_prune.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_prune.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm_geometry.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm_setup.cpp
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp: In function 'void nbnxn_put_on_grid(nonbonded_verlet_t*, const real (*)[3], int, const real*, const real*, const gmx::UpdateGroupsCog*, gmx::Range<int>, real, gmx::ArrayRef<const int>, gmx::ArrayRef<const gmx::BasicVector<double> >, int, const int*)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:57:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
57 | void nbnxn_put_on_grid(nonbonded_verlet_t* nb_verlet,
| ^~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:53:
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairsearch.h:184:27: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
184 | gridSet_.putOnGrid(box, ddZone, lowerCorner, upperCorner, updateGroupsCog, atomRange,
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
185 | atomDensity, atomInfo, x, numAtomsMoved, move, nbat);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp: In function 'void nbnxn_put_on_grid_nonlocal(nonbonded_verlet_t*, const gmx_domdec_zones_t*, gmx::ArrayRef<const int>, gmx::ArrayRef<const gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:76:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
76 | void nbnxn_put_on_grid_nonlocal(nonbonded_verlet_t* nbv,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:90:26: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
90 | nbnxn_put_on_grid(nbv, nullptr, zone, c0, c1, nullptr,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
91 | { zones->cg_range[zone], zones->cg_range[zone + 1] }, -1, atomInfo, x, 0,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
92 | nullptr);
| ~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp: In member function 'void nonbonded_verlet_t::convertCoordinates(gmx::AtomLocality, bool, gmx::ArrayRef<const gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:126:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
126 | void nonbonded_verlet_t::convertCoordinates(const gmx::AtomLocality locality,
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:126:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp: In member function 'void nonbonded_verlet_t::atomdata_add_nbat_f_to_f(gmx::AtomLocality, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:159:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
159 | void nonbonded_verlet_t::atomdata_add_nbat_f_to_f(const gmx::AtomLocality locality,
| ^~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist_tuning.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairlistparams.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlistparams.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairlistset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlistset.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairsearch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairsearch.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/prunekerneldispatch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/prunekerneldispatch.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpcontext.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpmodule.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpwriter.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineinit.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinemodule.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodulemanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinemodulemanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlineoptionsmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineoptionsmodule.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist.cpp:38:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::PinningPolicy}; _Tp = NbnxnPairlistGpu; _Alloc = std::allocator<NbnxnPairlistGpu>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<NbnxnPairlistGpu>::iterator' {aka '__gnu_cxx::__normal_iterator<NbnxnPairlistGpu*, std::vector<NbnxnPairlistGpu> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In constructor 'PairlistSet::PairlistSet(gmx::InteractionLocality, const PairlistParams&)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<NbnxnPairlistGpu*, std::vector<NbnxnPairlistGpu> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<NbnxnPairlistGpu*, std::vector<NbnxnPairlistGpu> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineparser.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlineprogramcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineprogramcontext.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/filenm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/pargs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/shellcompletions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/shellcompletions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/viewit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/viewit.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/atomdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/atomdistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/box.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/cellsizes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/cellsizes.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/collect.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp: In function 'void low_set_ddbox(int, int, const int (*)[3], const real (*)[3], bool, gmx::ArrayRef<const gmx::BasicVector<double> >, tmpi_comm_* const*, gmx_ddbox_t*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:232:13: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
232 | static void low_set_ddbox(int numPbcDimensions,
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp: In function 'void set_ddbox(const gmx_domdec_t&, bool, const real (*)[3], bool, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx_ddbox_t*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:278:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
278 | void set_ddbox(const gmx_domdec_t& dd,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:291:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
291 | low_set_ddbox(dd.unitCellInfo.npbcdim, dd.unitCellInfo.numBoundedDimensions, &dd.nc, box,
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
292 | calculateUnboundedSize, xRef,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
293 | needToReduceCoordinateData ? &dd.mpi_comm_all : nullptr, ddbox);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:291:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp: In function 'void set_ddbox_cr(const t_commrec&, const int (*)[3], const t_inputrec&, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, gmx_ddbox_t*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:302:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
302 | void set_ddbox_cr(const t_commrec& cr,
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:311:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
311 | low_set_ddbox(ePBC2npbcdim(ir.ePBC), inputrec2nboundeddim(&ir), dd_nc, box, true, x, nullptr, ddbox);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/distribute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp: In function 'void dd_collect_vec(gmx_domdec_t*, const t_state*, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:228:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
228 | void dd_collect_vec(gmx_domdec_t* dd,
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:228:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp: In function 'void dd_collect_state(gmx_domdec_t*, const t_state*, t_state*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:291:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
291 | dd_collect_vec(dd, state_local, state_local->x, globalXRef);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:296:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
296 | dd_collect_vec(dd, state_local, state_local->v, globalVRef);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:301:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
301 | dd_collect_vec(dd, state_local, state_local->cg_p, globalCgpRef);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/dlb.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/dlbtiming.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_constraints.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_network.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp: In function 'void ddSendrecv(const gmx_domdec_t*, int, int, gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:118:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
118 | void ddSendrecv(const gmx_domdec_t* dd,
| ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:118:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:118:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp: In function 'void ddSendrecv(const gmx_domdec_t*, int, int, gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = gmx::BasicVector<double>]':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:118:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:118:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:118:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_setup.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'gmx_bool test_dd_cutoff(t_commrec*, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, real)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3156:17: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3156 | static gmx_bool test_dd_cutoff(t_commrec* cr, const matrix box, gmx::ArrayRef<const gmx::RVec> x, real cutoffRequested)
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3166:14: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3166 | set_ddbox(*dd, false, box, true, x, &ddbox);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'gmx_bool change_dd_cutoff(t_commrec*, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, real)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3228:10: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3228 | gmx_bool change_dd_cutoff(t_commrec* cr, const matrix box, gmx::ArrayRef<const gmx::RVec> x, real cutoffRequested)
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_setup.cpp: In function 'DDGridSetup getDDGridSetup(const gmx::MDLogger&, const t_commrec*, int, const gmx::DomdecOptions&, const DDSettings&, const DDSystemInfo&, real, const gmx_mtop_t&, const t_inputrec&, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, gmx_ddbox_t*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_setup.cpp:906:13: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
906 | DDGridSetup getDDGridSetup(const gmx::MDLogger& mdlog,
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_setup.cpp:934:21: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
934 | set_ddbox_cr(*cr, &numDomainsLegacyIvec, ir, box, xGlobal, ddbox);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_setup.cpp:938:21: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
938 | set_ddbox_cr(*cr, nullptr, ir, box, xGlobal, ddbox);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_specatomcomm.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In constructor 'gmx::DomainDecompositionBuilder::Impl::Impl(const gmx::MDLogger&, t_commrec*, const gmx::DomdecOptions&, const gmx::MdrunOptions&, bool, const gmx_mtop_t&, const t_inputrec&, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3045:1: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3045 | DomainDecompositionBuilder::Impl::Impl(const MDLogger& mdlog,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:2967:82: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2967 | gridSetupCellsizeLimit, mtop, ir, box, xGlobal, &ddbox);
| ^
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3091:92: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3091 | gridSetupCellsizeLimit, mtop_, ir_, box, xGlobal, &ddbox_);
| ^
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_topology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_topology.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In constructor 'gmx::DomainDecompositionBuilder::DomainDecompositionBuilder(const gmx::MDLogger&, t_commrec*, const gmx::DomdecOptions&, const gmx::MdrunOptions&, bool, const gmx_mtop_t&, const t_inputrec&, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3134:1: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3134 | DomainDecompositionBuilder::DomainDecompositionBuilder(const MDLogger& mdlog,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3143:95: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3143 | impl_(new Impl(mdlog, cr, options, mdrunOptions, prefer1DAnd1Pulse, mtop, ir, box, xGlobal))
| ^
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'void dd_atom_spread_real(gmx_domdec_t*, real*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:531:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
531 | ddSendrecv(dd, d, dddirBackward, sendBuffer, receiveBuffer);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:531:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:531:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_vsite.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'void dd_atom_sum_real(gmx_domdec_t*, real*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:595:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
595 | ddSendrecv(dd, d, dddirForward, sendBuffer, receiveBuffer);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:595:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:595:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'void dd_move_x(gmx_domdec_t*, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >, gmx_wallcycle*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:272:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
272 | void dd_move_x(gmx_domdec_t* dd, const matrix box, gmx::ArrayRef<gmx::RVec> x, gmx_wallcycle* wcycle)
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:349:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
349 | ddSendrecv(dd, d, dddirBackward, sendBuffer, receiveBuffer);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:349:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:349:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'void dd_move_f(gmx_domdec_t*, gmx::ForceWithShiftForces*, gmx_wallcycle*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:424:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
424 | ddSendrecv(dd, d, dddirForward, sendBuffer, receiveBuffer);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:424:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:424:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/dump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/dump.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/ga2la.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/ga2la.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/gpuhaloexchange_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/gpuhaloexchange_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/localatomset.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/localatomsetdata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/localatomsetmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/mdsetup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/mdsetup.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/partition.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/redistribute.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/utility.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/utility.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/domdec/utility.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/domdec/utility.cpp:45:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/domdec/utility.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/domdec/utility.cpp:45:
/usr/include/c++/9/bits/stl_vector.h: In function 'void dd_resize_state(t_state*, PaddedHostVector<gmx::BasicVector<double> >*, int)':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/3dtransforms.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp: In function 'void dd_move_cellx(gmx_domdec_t*, const gmx_ddbox_t*, real*, real*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:253:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
253 | ddSendrecv(dd, d, dddirBackward, gmx::arrayRefFromArray(&buf_s[0].min0, numReals),
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
254 | gmx::arrayRefFromArray(&buf_r[0].min0, numReals));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:253:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:253:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/coordinatetransformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/densityfit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/densityfit.cpp
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function 'void gmx::ScaleCoordinates::Impl::scale(gmx::ArrayRef<gmx::BasicVector<double> >) const':
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:65:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
65 | void ScaleCoordinates::Impl::scale(ArrayRef<RVec> coordinates) const
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function 'void gmx::ScaleCoordinates::Impl::inverseIgnoringZeroScale(gmx::ArrayRef<gmx::BasicVector<double> >) const':
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:75:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
75 | void ScaleCoordinates::Impl::inverseIgnoringZeroScale(ArrayRef<RVec> coordinates) const
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function 'void gmx::ScaleCoordinates::operator()(gmx::ArrayRef<gmx::BasicVector<double> >) const':
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:97:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
97 | void ScaleCoordinates::operator()(ArrayRef<RVec> coordinates) const
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:99:17: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
99 | impl_->scale(coordinates);
| ~~~~~~~~~~~~^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function 'void gmx::ScaleCoordinates::inverseIgnoringZeroScale(gmx::ArrayRef<gmx::BasicVector<double> >) const':
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:102:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
102 | void ScaleCoordinates::inverseIgnoringZeroScale(ArrayRef<RVec> coordinates) const
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:104:36: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
104 | impl_->inverseIgnoringZeroScale(coordinates);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function 'void gmx::TranslateAndScale::Impl::transform(gmx::ArrayRef<gmx::BasicVector<double> >) const':
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:140:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
140 | void TranslateAndScale::Impl::transform(ArrayRef<RVec> coordinates) const
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function 'void gmx::TranslateAndScale::operator()(gmx::ArrayRef<gmx::BasicVector<double> >) const':
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:161:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
161 | void TranslateAndScale::operator()(ArrayRef<RVec> coordinates) const
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:163:21: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
163 | impl_->transform(coordinates);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/densityfittingforce.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/densityfittingforce.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/domdec/partition.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:46:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_range_insert(std::vector<_Tp, _Alloc>::iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/9/bits/vector.tcc:721:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >'} changed in GCC 7.1
721 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:721:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:721:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/domdec/partition.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:46:
/usr/include/c++/9/bits/stl_vector.h: In function 'void setup_dd_communication(gmx_domdec_t*, real (*)[3], gmx_ddbox_t*, t_forcerec*, t_state*, PaddedHostVector<gmx::BasicVector<double> >*)':
/usr/include/c++/9/bits/stl_vector.h:1662:4: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >'} changed in GCC 7.1
1662 | _M_range_insert(__pos, __first, __last,
| ^~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1662:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2104:34: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
2104 | ddSendrecv<gmx::RVec>(dd, dim_ind, dddirBackward, work.positionBuffer, rvecBufferRef);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2104:34: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2104:34: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/do_fit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/do_fit.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/exponentialmovingaverage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/exponentialmovingaverage.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/functions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/functions.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp: In function 'void dd_partition_system(FILE*, const gmx::MDLogger&, int64_t, const t_commrec*, gmx_bool, int, t_state*, const gmx_mtop_t&, const t_inputrec*, gmx::ImdSession*, pull_t*, t_state*, PaddedHostVector<gmx::BasicVector<double> >*, gmx::MDAtoms*, gmx_localtop_t*, t_forcerec*, gmx_vsite_t*, gmx::Constraints*, t_nrnb*, gmx_wallcycle*, gmx_bool)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2866:18: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2866 | set_ddbox(*dd, true, DDMASTER(dd) ? state_global->box : nullptr, true, xGlobal, &ddbox);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2907:18: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2907 | set_ddbox(*dd, bMasterState, state_local->box, true, state_local->x, &ddbox);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2928:18: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2928 | set_ddbox(*dd, bMasterState, state_local->box, bNStGlobalComm, state_local->x, &ddbox);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2946:39: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2946 | comm->updateGroupsCog->addCogs(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
2947 | gmx::arrayRefFromArray(dd->globalAtomGroupIndices.data(), dd->ncg_home), state_local->x);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2946:39: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2970:43: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2970 | comm->updateGroupsCog->addCogs(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
2971 | gmx::arrayRefFromArray(dd->globalAtomGroupIndices.data(), dd->ncg_home),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2972 | state_local->x);
| ~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2970:43: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:3005:26: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3005 | nbnxn_put_on_grid(fr->nbv.get(), state_local->box, 0, comm->zones.size[0].bb_x0,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
3006 | comm->zones.size[0].bb_x1, comm->updateGroupsCog.get(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
3007 | { 0, dd->ncg_home }, comm->zones.dens_zone0, fr->cginfo, state_local->x,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
3008 | ncg_moved, bRedist ? comm->movedBuffer.data() : nullptr);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/gausstransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/gausstransform.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/invertmatrix.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/units.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/units.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/utilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/utilities.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/veccompare.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/veccompare.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/vecdump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/vecdump.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/df_history.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/group.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/iforceprovider.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -Wno-class-memaccess -o CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/inputrec.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/md_enums.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/observableshistory.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpformat.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp: In function 'real (* makeRvecArray(gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::index))[3]':
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:208:7: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
208 | rvec* makeRvecArray(gmx::ArrayRef<const gmx::RVec> v, gmx::index n)
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp: In function 'void initialize_lambdas(FILE*, const t_inputrec&, bool, int*, gmx::ArrayRef<double>, double*)':
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:282:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
282 | void initialize_lambdas(FILE* fplog,
| ^~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:40:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:40:
/usr/include/c++/9/bits/stl_vector.h: In function 'void init_gtc_state(t_state*, int, int, int)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:40:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:40:
/usr/include/c++/9/bits/stl_vector.h: In function 'void state_change_natoms(t_state*, int)':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helptopic.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpwritercontext.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/rstparser.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/boxutilities.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/mshift.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp: In function 'void put_atoms_in_box(int, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp:1394:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1394 | void put_atoms_in_box(int ePBC, const matrix box, gmx::ArrayRef<gmx::RVec> x)
| ^~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc_simd.cpp
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp: In function 'void put_atoms_in_box_omp(int, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >, int)':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp:1454:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1454 | void put_atoms_in_box_omp(int ePBC, const matrix box, gmx::ArrayRef<gmx::RVec> x, gmx_unused int nth)
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp: In function 'void put_atoms_in_triclinic_unitcell(int, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp:1470:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1470 | void put_atoms_in_triclinic_unitcell(int ecenter, const matrix box, gmx::ArrayRef<gmx::RVec> x)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp: In function 'void put_atoms_in_compact_unitcell(int, int, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp:1527:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1527 | void put_atoms_in_compact_unitcell(int ePBC, int ecenter, const matrix box, gmx::ArrayRef<gmx::RVec> x)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp:1527:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcenums.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/rmpbc.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/random/seed.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/seed.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tabulatednormaldistribution.cpp
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp: In function 'void put_molecule_com_in_box(int, int, t_block*, int, t_atom*, int, real (*)[3], real (*)[3])':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp:289:46: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
289 | put_atoms_in_compact_unitcell(ePBC, ecenter, box, newComArrayRef);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp:289:46: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp: In function 'void put_residue_com_in_box(int, int, int, t_atom*, int, real (*)[3], real (*)[3])':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp:341:50: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
341 | put_atoms_in_compact_unitcell(ePBC, ecenter, box, newComArrayRef);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp:341:50: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp:341:50: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp:341:50: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/forcetable.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp: In constructor 'gmx::CubicSplineTable::CubicSplineTable(std::initializer_list<gmx::NumericalSplineTableInput>, const std::pair<double, double>&, real)':
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp:383:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
383 | CubicSplineTable::CubicSplineTable(std::initializer_list<NumericalSplineTableInput> numericalInputList,
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp:383:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp: In constructor 'gmx::QuadraticSplineTable::QuadraticSplineTable(std::initializer_list<gmx::NumericalSplineTableInput>, const std::pair<double, double>&, real)':
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp:367:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
367 | QuadraticSplineTable::QuadraticSplineTable(std::initializer_list<NumericalSplineTableInput> numericalInputList,
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp:170:99: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
170 | std::vector<double> thirdDerivative(internal::vectorSecondDerivative(derivative, inputSpacing));
| ^
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/cyclecounter.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/wallcycle.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/walltime_accounting.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atomprop.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'real gmx::internal::findSmallestQuotientOfFunctionAndSecondDerivative(gmx::ArrayRef<const double>, double, const std::pair<double, double>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:211:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
211 | real findSmallestQuotientOfFunctionAndSecondDerivative(ArrayRef<const double> function,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'real gmx::internal::findSmallestQuotientOfFunctionAndThirdDerivative(gmx::ArrayRef<const double>, double, const std::pair<double, double>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:291:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
291 | real findSmallestQuotientOfFunctionAndThirdDerivative(ArrayRef<const double> function,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'std::vector<double> gmx::internal::vectorSecondDerivative(gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:310:21: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
310 | std::vector<double> vectorSecondDerivative(ArrayRef<const double> f, double spacing)
| ^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'void gmx::internal::throwUnlessDerivativeIsConsistentWithFunction(gmx::ArrayRef<const double>, gmx::ArrayRef<const double>, double, const std::pair<double, double>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:112:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
112 | void throwUnlessDerivativeIsConsistentWithFunction(ArrayRef<const double> function,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:112:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/atoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atoms.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/utility/fatalerror.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/topology/atomprop.cpp:53:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {BaseEntry}; _Tp = BaseEntry; _Alloc = std::allocator<BaseEntry>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<BaseEntry>::iterator' {aka '__gnu_cxx::__normal_iterator<BaseEntry*, std::vector<BaseEntry> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In function 'void readProperty(AtomProperty*, ResidueType*, double)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BaseEntry*, std::vector<BaseEntry> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atomsbuilder.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/block.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/block.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/exclusionblocks.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/forcefieldparameters.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/idef.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/idef.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/ifunc.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/index.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/index.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/invblock.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/invblock.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/mtop_util.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/residuetypes.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/symtab.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/symtab.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/topology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/topology.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/topsort.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/topsort.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/swap/swapcoords.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/essentialdynamics/edsam.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pulling/output.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/output.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/swap/swapcoords.cpp:52:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::LocalAtomSet}; _Tp = swap_group; _Alloc = std::allocator<swap_group>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<swap_group>::iterator' {aka '__gnu_cxx::__normal_iterator<swap_group*, std::vector<swap_group> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In function 't_swap* init_swapcoords(FILE*, const t_inputrec*, const char*, gmx_mtop_t*, const t_state*, ObservablesHistory*, t_commrec*, gmx::LocalAtomSetManager*, const gmx_output_env_t*, const gmx::MdrunOptions&, gmx::StartingBehavior)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<swap_group*, std::vector<swap_group> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pulling/pull.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pulling/pull_rotation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pull_rotation.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/essentialdynamics/edsam.cpp:48:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {edpar&}; _Tp = edpar; _Alloc = std::allocator<edpar>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<edpar>::iterator' {aka '__gnu_cxx::__normal_iterator<edpar*, std::vector<edpar> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<edpar>::iterator' {aka '__gnu_cxx::__normal_iterator<edpar*, std::vector<edpar> >'} changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In function 'std::vector<edpar> {anonymous}::read_edi_file(const char*, int)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<edpar*, std::vector<edpar> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:39:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_pull_coord&}; _Tp = pull_coord_work_t; _Alloc = std::allocator<pull_coord_work_t>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pull_coord_work_t>::iterator' {aka '__gnu_cxx::__normal_iterator<pull_coord_work_t*, std::vector<pull_coord_work_t> >'} changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_pull_group&, gmx::LocalAtomSet, const bool&}; _Tp = pull_group_work_t; _Alloc = std::allocator<pull_group_work_t>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' {aka '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >'} changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_pull_group&, const gmx::LocalAtomSet&, bool&}; _Tp = pull_group_work_t; _Alloc = std::allocator<pull_group_work_t>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' {aka '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >'} changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In function 'pull_t* init_pull(FILE*, const pull_params_t*, const t_inputrec*, const gmx_mtop_t*, const t_commrec*, gmx::LocalAtomSetManager*, real)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pull_coord_work_t*, std::vector<pull_coord_work_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:39:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:39:
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2280:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' {aka '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >'} changed in GCC 7.1
2280 | }
| ^
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2280:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' {aka '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >'} changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2280:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' {aka '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >'} changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2280:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' {aka '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >'} changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp: In function 'bool pullCheckPbcWithinGroup(const pull_t&, gmx::ArrayRef<const gmx::BasicVector<double> >, const t_pbc&, int, real)':
/<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:949:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
949 | bool pullCheckPbcWithinGroup(const pull_t& pull,
| ^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:949:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/awh.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/awh.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/gmxlib/network.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:45:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/gmxlib/network.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:45:
/usr/include/c++/9/bits/stl_vector.h: In function 'void allocStatePrevStepPullCom(t_state*, const pull_t*)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/bias.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/biasparams.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biasparams.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.cpp:47:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, const double&, const double&}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >'} changed in GCC 7.1
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/biasparams.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/awh/biasparams.cpp:47:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In constructor 'gmx::BiasParams::BiasParams(const gmx::AwhParams&, const gmx::AwhBiasParams&, const std::vector<gmx::DimParams>&, double, double, gmx::BiasParams::DisableUpdateSkips, int, const std::vector<gmx::GridAxis>&, int)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp: In member function 'void gmx::Bias::updateForceCorrelationGrid(gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:386:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
386 | void Bias::updateForceCorrelationGrid(gmx::ArrayRef<const double> probWeightNeighbor, double t)
| ^~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:406:45: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
406 | state_.calcUmbrellaForceAndPotential(dimParams_, grid_, indexNeighbor, forceFromNeighbor);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:70:
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationgrid.h:104:37: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
104 | tensors_[pointIndex].addData(weight, data, blockLengthMeasure == BlockLengthMeasure::Weight, t);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp: In member function 'gmx::ArrayRef<const double> gmx::Bias::calcForceAndUpdateBias(const double*, double*, double*, const t_commrec*, const gmx_multisim_t*, double, int64_t, int64_t, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:144:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
144 | updateForceCorrelationGrid(probWeightNeighbor, t);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
162 | state_.calcConvolvedForce(dimParams_, grid_, probWeightNeighbor, tempForce_, biasForce_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:172:57: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
172 | potential = state_.calcUmbrellaForceAndPotential(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
173 | dimParams_, grid_, coordState.umbrellaGridpoint(), biasForce_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
182 | double newPotential = state_.moveUmbrella(dimParams_, grid_, probWeightNeighbor,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
183 | biasForce_, step, seed, params_.biasIndex);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/biassharing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biassharing.cpp
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::Bias, std::vector<int, std::allocator<int> >&}; _Tp = gmx::BiasCoupledToSystem; _Alloc = std::allocator<gmx::BiasCoupledToSystem>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BiasCoupledToSystem>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BiasCoupledToSystem*, std::vector<gmx::BiasCoupledToSystem> >'} changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/biasstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp
/usr/include/c++/9/bits/vector.tcc: In constructor 'gmx::Awh::Awh(FILE*, const t_inputrec&, const t_commrec*, const gmx_multisim_t*, const gmx::AwhParams&, const string&, pull_t*)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BiasCoupledToSystem*, std::vector<gmx::BiasCoupledToSystem> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/biaswriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biaswriter.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/coordstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/coordstate.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In function 'void gmx::{anonymous}::updateTargetDistribution(gmx::ArrayRef<gmx::PointState>, const gmx::BiasParams&)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:292:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::PointState>' changed in GCC 7.1
292 | void updateTargetDistribution(gmx::ArrayRef<PointState> pointState, const BiasParams& params)
| ^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'double gmx::BiasState::calcUmbrellaForceAndPotential(const std::vector<gmx::DimParams>&, const gmx::Grid&, int, gmx::ArrayRef<double>) const':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:416:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
416 | double BiasState::calcUmbrellaForceAndPotential(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::calcConvolvedForce(const std::vector<gmx::DimParams>&, const gmx::Grid&, gmx::ArrayRef<const double>, gmx::ArrayRef<double>, gmx::ArrayRef<double>) const':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:437:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
437 | void BiasState::calcConvolvedForce(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:437:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:437:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:457:38: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
457 | calcUmbrellaForceAndPotential(dimParams, grid, indexNeighbor, forceFromNeighbor);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'double gmx::BiasState::moveUmbrella(const std::vector<gmx::DimParams>&, const gmx::Grid&, gmx::ArrayRef<const double>, gmx::ArrayRef<double>, int64_t, int64_t, int)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:467:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
467 | double BiasState::moveUmbrella(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:467:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:467:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:476:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
476 | coordState_.sampleUmbrellaGridpoint(grid, coordState_.gridpointIndex(), probWeightNeighbor,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
477 | step, seed, indexSeed);
| ~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:476:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:481:42: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
481 | calcUmbrellaForceAndPotential(dimParams, grid, coordState_.umbrellaGridpoint(), newForce);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/coordstate.cpp: In member function 'void gmx::CoordState::sampleUmbrellaGridpoint(const gmx::Grid&, int, gmx::ArrayRef<const double>, int64_t, int64_t, int)':
/<<PKGBUILDDIR>>/src/gromacs/awh/coordstate.cpp:129:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
129 | void CoordState::sampleUmbrellaGridpoint(const Grid& grid,
| ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::sampleProbabilityWeights(const gmx::Grid&, gmx::ArrayRef<const double>)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1233:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1233 | void BiasState::sampleProbabilityWeights(const Grid& grid, gmx::ArrayRef<const double> probWeightNeighbor)
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::sampleCoordAndPmf(const gmx::Grid&, gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1287:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1287 | void BiasState::sampleCoordAndPmf(const Grid& grid, gmx::ArrayRef<const double> probWeightNeighbor, double convolvedBias)
| ^~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/correlationgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/correlationgrid.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/correlationhistory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/correlationhistory.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::updateFreeEnergyAndAddSamplesToHistogram(const std::vector<gmx::DimParams>&, const gmx::Grid&, const gmx::BiasParams&, const t_commrec*, const gmx_multisim_t*, double, int64_t, FILE*, std::vector<int>*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
1072 | double newHistogramSize = histogramSize_.newHistogramSize(params, t, detectedCovering, points_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1073 | weightSumCovering_, fplog);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/correlationtensor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/grid.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/histogramsize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp: In member function 'void gmx::CorrelationTensor::addData(double, gmx::ArrayRef<const double>, bool, double)':
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp:229:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
229 | void CorrelationTensor::addData(double weight, gmx::ArrayRef<const double> data, bool blockLengthInWeight, double t)
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp:229:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp:47:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {int&, double}; _Tp = gmx::CorrelationBlockData; _Alloc = std::allocator<gmx::CorrelationBlockData>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::CorrelationBlockData>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::CorrelationBlockData*, std::vector<gmx::CorrelationBlockData> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In constructor 'gmx::CorrelationTensor::CorrelationTensor(int, int, double)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::CorrelationBlockData*, std::vector<gmx::CorrelationBlockData> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp: In member function 'double gmx::HistogramSize::newHistogramSizeInitialStage(const gmx::BiasParams&, double, bool, gmx::ArrayRef<double>, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp:77:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
77 | double HistogramSize::newHistogramSizeInitialStage(const BiasParams& params,
| ^~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/pointstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/pointstate.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp: In member function 'double gmx::HistogramSize::newHistogramSize(const gmx::BiasParams&, double, bool, const std::vector<gmx::PointState>&, gmx::ArrayRef<double>, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp:209:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
209 | double HistogramSize::newHistogramSize(const BiasParams& params,
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp:242:56: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
242 | newHistogramSize = newHistogramSizeInitialStage(params, t, covered, weightsumCovering, fplog);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp:242:56: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/read_params.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/read_params.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/simd/support.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/support.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/dimparams.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/awh/grid.h:60,
from /<<PKGBUILDDIR>>/src/gromacs/awh/grid.cpp:47:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, double&, double&, double&}; _Tp = gmx::GridAxis; _Alloc = std::allocator<gmx::GridAxis>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::GridAxis>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In constructor 'gmx::Grid::Grid(const std::vector<gmx::DimParams>&, const gmx::AwhDimParams*)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&, const double&, double, int&}; _Tp = gmx::GridAxis; _Alloc = std::allocator<gmx::GridAxis>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::GridAxis>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In function 'void gmx::mapGridToDataGrid(std::vector<int>*, const double* const*, int, const string&, const gmx::Grid&, const string&)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/imd/imd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/imd/imd.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/imd/imdsocket.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/anadih.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/anadih.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/angle_correction.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/angle_correction.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/binsearch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/binsearch.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/cmat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/cmat.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/dens_filter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/dens_filter.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/dlist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/dlist.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/eigio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/eigio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/fitahx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/fitahx.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_anaeig.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_anaeig.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_analyze.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_analyze.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_angle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_angle.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_awh.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_awh.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_bar.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_bar.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_awh.cpp:54:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_awh.cpp:54:
/usr/include/c++/9/bits/stl_vector.h: In function 'int gmx_awh(int, char**)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_bundle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_bundle.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_chi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_chi.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_cluster.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_cluster.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_clustsize.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_confrms.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_covar.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_current.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_density.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_densmap.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_densorder.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_dielectric.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_dielectric.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_dipoles.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_dipoles.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_disre.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_disre.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_do_dssp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_do_dssp.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_do_dssp.cpp:47:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_mapping&}; _Tp = t_mapping; _Alloc = std::allocator<t_mapping>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_mapping>::iterator' {aka '__gnu_cxx::__normal_iterator<t_mapping*, std::vector<t_mapping> >'} changed in GCC 7.1
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_do_dssp.cpp:47:
/usr/include/c++/9/bits/stl_vector.h: In function 'int gmx_do_dssp(int, char**)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_do_dssp.cpp:47:
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_mapping*, std::vector<t_mapping> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_dos.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_dos.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_dyecoupl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_dyecoupl.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_enemat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_enemat.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_energy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_energy.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_filter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_filter.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_gyrate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_gyrate.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_h2order.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_h2order.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_hbond.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_hbond.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_helix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_helix.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_helixorient.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_helixorient.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_hydorder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_hydorder.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_lie.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_lie.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_make_edi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_make_edi.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_mdmat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_mdmat.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_mindist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_mindist.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_msd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_msd.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmeig.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_nmeig.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmens.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_nmens.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_msd.cpp:44:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_msd.cpp:44:
/usr/include/c++/9/bits/stl_vector.h: In constructor 't_corr::t_corr(int, int, int, real, int, gmx_bool, gmx_bool, real, const t_topology*, real, real)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_nmr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmtraj.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_nmtraj.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_nmtraj.cpp:44:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {int}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_order.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_order.cpp
/usr/include/c++/9/bits/vector.tcc: In function 'int gmx_nmtraj(int, char**)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_nmtraj.cpp:44:
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_polystat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_polystat.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_potential.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_potential.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_velacc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_velacc.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_wham.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_wham.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_wheel.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_wheel.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_xpm2ps.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/hxprops.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/hxprops.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp: In function 'void rainbow_map(gmx_bool, gmx::ArrayRef<t_mapping>)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:1328:13: note: parameter passing for argument of type 'gmx::ArrayRef<t_mapping>' changed in GCC 7.1
1328 | static void rainbow_map(gmx_bool bBlue, gmx::ArrayRef<t_mapping> map)
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp: In function 'void leg_continuous(t_psdata*, real, real, real, const string&, real, char*, gmx::ArrayRef<const t_mapping>, int)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:249:13: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
249 | static void leg_continuous(t_psdata* ps,
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp: In function 'void ps_mat(const char*, gmx::ArrayRef<t_matrix>, gmx::ArrayRef<t_matrix>, gmx_bool, gmx_bool, gmx_bool, gmx_bool, gmx_bool, gmx_bool, int, real, real, real, const char*, const char*, int)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:1033:31: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
1033 | leg_continuous(&out, x0 + w / 2, w / 2, DDD, legend, psr->legfontsize, psr->legfont,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1034 | leg_map, mapoffset);
| ~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:1033:31: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:316:19: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
316 | leg_continuous(ps, xx1, x1, y0, label1, fontsize, font, map1, 0);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:316:19: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:317:19: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
317 | leg_continuous(ps, xx2, x2, y0, label2, fontsize, font, map2, 0);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:317:19: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/nrama.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/nrama.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/nsfactor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/nsfactor.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp: In function 'int gmx_xpm2ps(int, char**)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:1376:20: note: parameter passing for argument of type 'gmx::ArrayRef<t_mapping>' changed in GCC 7.1
1376 | rainbow_map(bBlue, m.map);
| ~~~~~~~~~~~^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:1376:20: note: parameter passing for argument of type 'gmx::ArrayRef<t_mapping>' changed in GCC 7.1
1376 | rainbow_map(bBlue, m.map);
| ~~~~~~~~~~~^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/powerspect.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/powerspect.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/pp2shift.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/pp2shift.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/princ.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/princ.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/sfactor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/sfactor.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/thermochemistry.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp: In function 'double calcZeroPointEnergy(gmx::ArrayRef<const double>, real)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp:53:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
53 | double calcZeroPointEnergy(gmx::ArrayRef<const real> eigval, real scale_factor)
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp: In function 'double calcVibrationalInternalEnergy(gmx::ArrayRef<const double>, real, gmx_bool, real)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp:66:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
66 | double calcVibrationalInternalEnergy(gmx::ArrayRef<const real> eigval, real temperature, gmx_bool linear, real scale_factor)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp: In function 'double calcVibrationalHeatCapacity(gmx::ArrayRef<const double>, real, gmx_bool, real)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp:93:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
93 | double calcVibrationalHeatCapacity(gmx::ArrayRef<const real> eigval, real temperature, gmx_bool linear, real scale_factor)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp: In function 'double calcQuasiHarmonicEntropy(gmx::ArrayRef<const double>, real, gmx_bool, real)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp:158:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
158 | double calcQuasiHarmonicEntropy(gmx::ArrayRef<const real> eigval, real temperature, gmx_bool bLinear, real scale_factor)
| ^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp: In function 'double calcSchlitterEntropy(gmx::ArrayRef<const double>, real, gmx_bool)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp:185:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
185 | double calcSchlitterEntropy(gmx::ArrayRef<const real> eigval, real temperature, gmx_bool bLinear)
| ^~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/add_par.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/calch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/calch.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/convparm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/convparm.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/editconf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/editconf.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:40:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {InteractionOfType}; _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<InteractionOfType>::iterator' {aka '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp: In function 'void add_param(InteractionsOfType*, int, int, gmx::ArrayRef<const double>, const char*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:55:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
55 | void add_param(InteractionsOfType* ps, int ai, int aj, gmx::ArrayRef<const real> c, const char* s)
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:64:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
64 | ps->interactionTypes.emplace_back(InteractionOfType(atoms, forceParm, s ? s : ""));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:64:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:40:
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp: In function 'void add_vsite4_atoms(InteractionsOfType*, int, int, int, int, int)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:101:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
101 | ps->interactionTypes.emplace_back(InteractionOfType(atoms, {}));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:101:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:40:
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp: In function 'void add_cmap_param(InteractionsOfType*, int, int, int, int, int, const char*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:70:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
70 | ps->interactionTypes.emplace_back(InteractionOfType(atoms, {}, s ? s : ""));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:70:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:40:
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp: In function 'void add_vsite3_atoms(InteractionsOfType*, int, int, int, int, bool)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:90:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
90 | ps->interactionTypes.emplace_back(InteractionOfType(atoms, {}));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:90:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:40:
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp: In function 'void add_vsite2_param(InteractionsOfType*, int, int, int, real)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:77:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
77 | ps->interactionTypes.emplace_back(InteractionOfType(atoms, forceParm));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:77:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:40:
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp: In function 'void add_vsite3_param(InteractionsOfType*, int, int, int, int, real, real)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:84:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
84 | ps->interactionTypes.emplace_back(InteractionOfType(atoms, forceParm));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:84:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:40:
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/fflibutil.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/convparm.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/convparm.cpp:40:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_iparams&}; _Tp = t_iparams; _Alloc = std::allocator<t_iparams>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_iparams>::iterator' {aka '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/convparm.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/convparm.cpp:40:
/usr/include/c++/9/bits/stl_vector.h: In function 'void enter_function(const InteractionsOfType*, t_functype, int, real, gmx_ffparams_t*, InteractionList*, bool, bool)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In function 'void convertInteractionsOfType(int, gmx::ArrayRef<const InteractionsOfType>, gmx::ArrayRef<const MoleculeInformation>, const MoleculeInformation*, int, double, real, gmx_mtop_t*)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_maxwell_velocities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_maxwell_velocities.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_vsite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:40:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const InteractionOfType&}; _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<InteractionOfType>::iterator' {aka '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair<InteractionOfType, int>}; _Tp = std::pair<InteractionOfType, int>; _Alloc = std::allocator<std::pair<InteractionOfType, int> >]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<std::pair<InteractionOfType, int> >::iterator' {aka '__gnu_cxx::__normal_iterator<std::pair<InteractionOfType, int>*, std::vector<std::pair<InteractionOfType, int> > >'} changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp: In function 'std::vector<InteractionOfType> clean_dih(gmx::ArrayRef<const InteractionOfType>, gmx::ArrayRef<const InteractionOfType>, t_atoms*, bool, bool)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:252:39: note: parameter passing for argument of type 'gmx::ArrayRef<const InteractionOfType>' changed in GCC 7.1
252 | static std::vector<InteractionOfType> clean_dih(gmx::ArrayRef<const InteractionOfType> dih,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:252:39: note: parameter passing for argument of type 'gmx::ArrayRef<const InteractionOfType>' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:40:
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<InteractionOfType, int>*, std::vector<std::pair<InteractionOfType, int> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<InteractionOfType, int>*, std::vector<std::pair<InteractionOfType, int> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/genconf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genconf.cpp
In file included from /usr/include/c++/9/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:47:
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]':
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp: In function 'int gen_vsites_6ring(t_atoms*, int**, gmx::ArrayRef<InteractionsOfType>, int, int*, real, real, real, bool)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
637 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
637 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
637 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:47:
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Distance = int; _Tp = InteractionOfType; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]':
/usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]':
/usr/include/c++/9/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
326 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__pop_heap(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]':
/usr/include/c++/9/bits/stl_heap.h:243:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
243 | __pop_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h:243:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_heap.h:243:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
In file included from /usr/include/c++/9/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:47:
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]':
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1939 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
In file included from /usr/include/c++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:47:
/usr/include/c++/9/bits/stl_heap.h:408:19: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
408 | std::__pop_heap(__first, __last, __last, __comp);
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:47:
/usr/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1671:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1671 | std::__make_heap(__first, __middle, __comp);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp: In function 'int gen_vsites_his(t_atoms*, int**, gmx::ArrayRef<InteractionsOfType>, int, int*, gmx::ArrayRef<const VirtualSiteTopology>)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
637 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
637 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp: In function 'void gen_pad(t_atoms*, gmx::ArrayRef<const PreprocessResidue>, gmx::ArrayRef<InteractionsOfType>, t_excls*, gmx::ArrayRef<MoleculePatchDatabase>, bool)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:674:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
674 | ang.push_back(InteractionOfType(atomNumbers, {}, name));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:674:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:725:63: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
725 | dih.push_back(InteractionOfType(atomNumbers, {}, name));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:725:63: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:735:51: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
735 | dih.push_back(InteractionOfType(atoms, {}, ""));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:735:51: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:754:59: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
754 | pai.push_back(InteractionOfType(atoms, {}, ""));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:754:59: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:809:35: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
809 | ang.push_back(InteractionOfType(atomNumbers, {}, bondeds.s));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:809:35: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:847:35: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
847 | dih.push_back(InteractionOfType(atomNumbers, {}, bondeds.s));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:847:35: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/9/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:47:
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:888:24: note: parameter passing for argument of type 'gmx::ArrayRef<const InteractionOfType>' changed in GCC 7.1
888 | dih = clean_dih(dih, improper, atoms, rtpFFDB[0].bKeepAllGeneratedDihedrals,
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
889 | rtpFFDB[0].bRemoveDihedralIfWithImproper);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:888:24: note: parameter passing for argument of type 'gmx::ArrayRef<const InteractionOfType>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:888:24: note: parameter passing for argument of type 'gmx::ArrayRef<const InteractionOfType>' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:40:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:389:43: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
389 | improper.emplace_back(InteractionOfType(ai, {}, bondeds.s));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:389:43: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/genhydro.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genhydro.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp: In function 'int gen_vsites_trp(PreprocessingAtomTypes*, std::vector<gmx::BasicVector<double> >*, t_atom**, char****, int**, int**, int**, t_symtab*, int*, gmx::ArrayRef<const gmx::BasicVector<double> >, int**, t_atoms*, int**, gmx::ArrayRef<InteractionsOfType>, int, int*, int, gmx::ArrayRef<const VirtualSiteTopology>)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
637 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
637 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
637 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genhydro.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genhydro.cpp:39:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const MoleculePatch&}; _Tp = MoleculePatch; _Alloc = std::allocator<MoleculePatch>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<MoleculePatch>::iterator' {aka '__gnu_cxx::__normal_iterator<MoleculePatch*, std::vector<MoleculePatch> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp: In function 'int gen_vsites_tyr(PreprocessingAtomTypes*, std::vector<gmx::BasicVector<double> >*, t_atom**, char****, int**, int**, int**, t_symtab*, int*, gmx::ArrayRef<const gmx::BasicVector<double> >, int**, t_atoms*, int**, gmx::ArrayRef<InteractionsOfType>, int, int*, int, gmx::ArrayRef<const VirtualSiteTopology>)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
637 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
637 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
637 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
637 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/genion.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genion.cpp
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genhydro.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genhydro.cpp:39:
/usr/include/c++/9/bits/stl_vector.h: In function 'void expand_hackblocks_one(const MoleculePatchDatabase&, std::string, std::vector<MoleculePatch>*, bool, bool)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<MoleculePatch*, std::vector<MoleculePatch> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp: In function 'void do_vsites(gmx::ArrayRef<const PreprocessResidue>, PreprocessingAtomTypes*, t_atoms*, t_symtab*, std::vector<gmx::BasicVector<double> >*, gmx::ArrayRef<InteractionsOfType>, int**, int**, real, bool, const char*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
637 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
637 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
637 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
637 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:2247:21: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
2247 | *parm = InteractionOfType(newAtomNumber, parm->forceParam(), parm->interactionTypeName());
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:2247:21: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/genrestr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genrestr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/gmxcpp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gmxcpp.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_atomtype.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_bond_atomtype.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_bond_atomtype.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_nextnb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_nextnb.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.cpp:39:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_atom&, char**, const InteractionOfType&, int&, int&}; _Tp = AtomTypeData; _Alloc = std::allocator<AtomTypeData>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<AtomTypeData>::iterator' {aka '__gnu_cxx::__normal_iterator<AtomTypeData*, std::vector<AtomTypeData> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'int PreprocessingAtomTypes::addType(t_symtab*, const t_atom&, const string&, const InteractionOfType&, int, int)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AtomTypeData*, std::vector<AtomTypeData> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::ArrayRef<const int>, gmx::ArrayRef<const double>, const std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&}; _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<InteractionOfType>::iterator' {aka '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/arm-linux-gnueabihf/c++/9/bits/c++allocator.h:33,
from /usr/include/c++/9/bits/allocator.h:46,
from /usr/include/c++/9/string:41,
from /usr/include/c++/9/stdexcept:39,
from /usr/include/c++/9/array:39,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.cpp:39:
/usr/include/c++/9/ext/new_allocator.h:147:4: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
147 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/ext/new_allocator.h:147:4: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.cpp:39:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const AtomTypeData&}; _Tp = AtomTypeData; _Alloc = std::allocator<AtomTypeData>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<AtomTypeData>::iterator' {aka '__gnu_cxx::__normal_iterator<AtomTypeData*, std::vector<AtomTypeData> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/arm-linux-gnueabihf/c++/9/bits/c++allocator.h:33,
from /usr/include/c++/9/bits/allocator.h:46,
from /usr/include/c++/9/string:41,
from /usr/include/c++/9/stdexcept:39,
from /usr/include/c++/9/array:39,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.cpp:39:
/usr/include/c++/9/ext/new_allocator.h: In member function 'void PreprocessingAtomTypes::renumberTypes(gmx::ArrayRef<InteractionsOfType>, gmx_mtop_t*, int*, bool)':
/usr/include/c++/9/ext/new_allocator.h:147:4: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
147 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/ext/new_allocator.h:147:4: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.cpp:39:
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.cpp:39:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AtomTypeData*, std::vector<AtomTypeData> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/grompp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/grompp.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/h_db.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/h_db.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/hackblock.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hackblock.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hackblock.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hackblock.cpp:40:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_atom&}; _Tp = t_atom; _Alloc = std::allocator<t_atom>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_atom>::iterator' {aka '__gnu_cxx::__normal_iterator<t_atom*, std::vector<t_atom> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hackblock.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hackblock.cpp:40:
/usr/include/c++/9/bits/stl_vector.h: In function 'void copyPreprocessResidues(const PreprocessResidue&, PreprocessResidue*, t_symtab*)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_atom*, std::vector<t_atom> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/grompp.cpp: In constructor 'InteractionOfType::InteractionOfType(gmx::ArrayRef<const int>, gmx::ArrayRef<const double>, const string&)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/grompp.cpp:111:1: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
111 | InteractionOfType::InteractionOfType(gmx::ArrayRef<const int> atoms,
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hackblock.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hackblock.cpp:40:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const MoleculePatch&}; _Tp = MoleculePatch; _Alloc = std::allocator<MoleculePatch>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<MoleculePatch>::iterator' {aka '__gnu_cxx::__normal_iterator<MoleculePatch*, std::vector<MoleculePatch> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hackblock.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hackblock.cpp:40:
/usr/include/c++/9/bits/stl_vector.h: In function 'void mergeAtomModifications(const MoleculePatchDatabase&, MoleculePatchDatabase*)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<MoleculePatch*, std::vector<MoleculePatch> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/h_db.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/h_db.cpp:40:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {MoleculePatch}; _Tp = MoleculePatch; _Alloc = std::allocator<MoleculePatch>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<MoleculePatch>::iterator' {aka '__gnu_cxx::__normal_iterator<MoleculePatch*, std::vector<MoleculePatch> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/hizzie.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hizzie.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/insert_molecules.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/insert_molecules.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/insert_molecules.cpp:45:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_range_insert(std::vector<_Tp, _Alloc>::iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/9/bits/vector.tcc:721:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >'} changed in GCC 7.1
721 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:721:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:721:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_range_insert(std::vector<_Tp, _Alloc>::iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator<const double*, std::vector<double> >; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:721:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:721:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:721:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In function 'void read_h_db_file(const char*, std::vector<MoleculePatchDatabase>*)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<MoleculePatch*, std::vector<MoleculePatch> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/insert_molecules.cpp:45:
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual int gmx::{anonymous}::InsertMolecules::run()':
/usr/include/c++/9/bits/stl_vector.h:1662:4: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >'} changed in GCC 7.1
1662 | _M_range_insert(__pos, __first, __last,
| ^~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1662:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_vector.h:1662:4: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
1662 | _M_range_insert(__pos, __first, __last,
| ^~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1662:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/makeexclusiondistances.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/makeexclusiondistances.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/nm2type.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/nm2type.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/makeexclusiondistances.h:38,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/makeexclusiondistances.cpp:37:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/makeexclusiondistances.h:38,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/makeexclusiondistances.cpp:37:
/usr/include/c++/9/bits/stl_vector.h: In function 'std::vector<double> makeExclusionDistances(const t_atoms*, AtomProperties*, real, real)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2gmx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2gmx.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2top.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/nm2type.cpp: In function 'int nm2type(int, t_nm2type*, t_symtab*, t_atoms*, PreprocessingAtomTypes*, int*, InteractionsOfType*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/nm2type.cpp:342:63: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
342 | k = atype->addType(tab, atoms->atom[i], type, InteractionOfType({}, {}),
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/nm2type.cpp:342:63: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/pgutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pgutil.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/readir.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readir.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:39:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_atom&}; _Tp = t_atom; _Alloc = std::allocator<t_atom>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_atom>::iterator' {aka '__gnu_cxx::__normal_iterator<t_atom*, std::vector<t_atom> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In function 'void add_atom_to_restp(PreprocessResidue*, t_symtab*, int, const MoleculePatch*)':
/usr/include/c++/9/bits/vector.tcc:161:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_atom*, std::vector<t_atom> >' changed in GCC 7.1
161 | _M_realloc_insert(begin() + (__position - cbegin()), __x);
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp: In function 'void match_atomnames_with_rtp(gmx::ArrayRef<PreprocessResidue>, gmx::ArrayRef<MoleculePatchDatabase>, t_atoms*, t_symtab*, gmx::ArrayRef<gmx::BasicVector<double> >, bool)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:1305:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1305 | void match_atomnames_with_rtp(gmx::ArrayRef<PreprocessResidue> usedPpResidues,
| ^~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2gmx.cpp:49:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const gmx::BasicVector<double>&}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double (&)[3]}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >'} changed in GCC 7.1
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2gmx.cpp:49:
/usr/include/c++/9/bits/stl_vector.h: In function 'void sort_pdbatoms(gmx::ArrayRef<const PreprocessResidue>, int, t_atoms**, t_atoms**, std::vector<gmx::BasicVector<double> >*, t_blocka*, char***)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:39:
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]':
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]':
/usr/include/c++/9/bits/stl_algo.h:1820:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1820 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:39:
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Distance = int; _Tp = InteractionOfType; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]':
/usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]':
/usr/include/c++/9/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
326 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__pop_heap(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]':
/usr/include/c++/9/bits/stl_heap.h:243:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
243 | __pop_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h:243:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_heap.h:243:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
In file included from /usr/include/c++/9/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:39:
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]':
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1939 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
In file included from /usr/include/c++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:39:
/usr/include/c++/9/bits/stl_heap.h:408:19: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
408 | std::__pop_heap(__first, __last, __last, __comp);
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:39:
/usr/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1671:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1671 | std::__make_heap(__first, __middle, __comp);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2gmx.cpp:49:
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual int gmx::{anonymous}::pdb2gmx::run()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2gmx.cpp:2149:33: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
2149 | match_atomnames_with_rtp(restp_chain, hb_chain, pdba, &symtab, x, bVerbose_);
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2gmx.cpp:49:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp: In function 'void pdb2top(FILE*, const char*, const char*, t_atoms*, std::vector<gmx::BasicVector<double> >*, PreprocessingAtomTypes*, t_symtab*, gmx::ArrayRef<const PreprocessResidue>, gmx::ArrayRef<PreprocessResidue>, gmx::ArrayRef<MoleculePatchDatabase>, bool, bool, bool, const char*, real, gmx::ArrayRef<const DisulfideBond>, real, real, bool, bool, bool, bool, bool)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:782:26: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
782 | add_param(psb, ai, aj, {}, patch.s.c_str());
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:782:26: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:796:38: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
796 | add_param(psb, i, i + 1, {}, nullptr); /* C-O */
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:796:38: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:797:38: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
797 | add_param(psb, i, i + 2, {}, nullptr); /* C-OA */
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:797:38: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:798:38: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
798 | add_param(psb, i + 2, i + 3, {}, nullptr); /* OA-H */
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:798:38: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:803:42: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
803 | add_param(psb, i, i + k + 1, {}, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:803:42: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:729:18: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
729 | add_param(ps, ai, aj, {}, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:729:18: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/9/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:39:
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/readpull.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readpull.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readpull.cpp: In function 'pull_t* set_pull_init(t_inputrec*, const gmx_mtop_t*, real (*)[3], real (*)[3], real, warninp_t)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readpull.cpp:553:53: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
553 | bool groupObeysPbc = pullCheckPbcWithinGroup(
| ~~~~~~~~~~~~~~~~~~~~~~~^
554 | *pull_work, gmx::arrayRefFromArray(reinterpret_cast<gmx::RVec*>(x), mtop->natoms),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
555 | pbc, g, c_pullGroupSmallGroupThreshold);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readpull.cpp:584:52: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
584 | groupObeysPbc = pullCheckPbcWithinGroup(
| ~~~~~~~~~~~~~~~~~~~~~~~^
585 | *pull_work, gmx::arrayRefFromArray(reinterpret_cast<gmx::RVec*>(x), mtop->natoms),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
586 | pbc, g, c_pullGroupPbcMargin);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/readrot.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readrot.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/resall.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/resall.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/solvate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/solvate.cpp
In file included from /usr/include/c++/9/vector:72,
from /usr/include/c++/9/bits/random.h:34,
from /usr/include/c++/9/random:49,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/solvate.cpp:44:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_range_insert(std::vector<_Tp, _Alloc>::iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/9/bits/vector.tcc:721:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >'} changed in GCC 7.1
721 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:721:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:721:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/specbond.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/specbond.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/resall.cpp: In function 'PreprocessingAtomTypes read_atype(const char*, t_symtab*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/resall.cpp:93:43: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
93 | at.addType(tab, *a, name, InteractionOfType({}, {}), 0, 0);
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/resall.cpp:93:43: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:67,
from /usr/include/c++/9/bits/random.h:34,
from /usr/include/c++/9/random:49,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/solvate.cpp:44:
/usr/include/c++/9/bits/stl_vector.h: In function 'int gmx_solvate(int, char**)':
/usr/include/c++/9/bits/stl_vector.h:1662:4: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >'} changed in GCC 7.1
1662 | _M_range_insert(__pos, __first, __last,
| ^~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1662:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_vector.h:1662:4: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >'} changed in GCC 7.1
1662 | _M_range_insert(__pos, __first, __last,
| ^~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1662:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/resall.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/resall.cpp:39:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {}; _Tp = t_atom; _Alloc = std::allocator<t_atom>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_atom>::iterator' {aka '__gnu_cxx::__normal_iterator<t_atom*, std::vector<t_atom> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_atom>::iterator' {aka '__gnu_cxx::__normal_iterator<t_atom*, std::vector<t_atom> >'} changed in GCC 7.1
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/specbond.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/specbond.cpp:39:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const SpecialBond&}; _Tp = SpecialBond; _Alloc = std::allocator<SpecialBond>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<SpecialBond>::iterator' {aka '__gnu_cxx::__normal_iterator<SpecialBond*, std::vector<SpecialBond> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/specbond.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/specbond.cpp:39:
/usr/include/c++/9/bits/stl_vector.h: In function 'std::vector<SpecialBond> generateSpecialBonds()':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SpecialBond*, std::vector<SpecialBond> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/ter_db.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/ter_db.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/tomorse.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tomorse.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/ter_db.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/ter_db.cpp:39:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {MoleculePatch}; _Tp = MoleculePatch; _Alloc = std::allocator<MoleculePatch>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<MoleculePatch>::iterator' {aka '__gnu_cxx::__normal_iterator<MoleculePatch*, std::vector<MoleculePatch> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {}; _Tp = t_atom; _Alloc = std::allocator<t_atom>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_atom>::iterator' {aka '__gnu_cxx::__normal_iterator<t_atom*, std::vector<t_atom> >'} changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In function 'void read_ter_db_file(const char*, std::vector<MoleculePatchDatabase>*, PreprocessingAtomTypes*)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<MoleculePatch*, std::vector<MoleculePatch> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_atom*, std::vector<t_atom> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tomorse.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tomorse.cpp:40:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {InteractionOfType}; _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<InteractionOfType>::iterator' {aka '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tomorse.cpp: In function 'void convert_harmonics(gmx::ArrayRef<MoleculeInformation>, PreprocessingAtomTypes*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tomorse.cpp:231:33: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
231 | InteractionOfType(atoms, forceParam));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tomorse.cpp:231:33: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tomorse.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tomorse.cpp:40:
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/topdirs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topdirs.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/topio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/toppush.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp
/usr/include/c++/9/bits/vector.tcc: In function 'void readResidueDatabase(const string&, std::vector<PreprocessResidue>*, PreprocessingAtomTypes*, t_symtab*, bool)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_atom*, std::vector<t_atom> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topio.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topio.cpp:39:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {InteractionOfType}; _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<InteractionOfType>::iterator' {aka '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/topshake.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topio.cpp: In function 'char** read_topol(const char*, const char*, const char*, const char*, t_symtab*, PreprocessingAtomTypes*, std::vector<MoleculeInformation>*, std::unique_ptr<MoleculeInformation>*, gmx::ArrayRef<InteractionsOfType>, int*, double*, t_gromppopts*, real*, std::vector<gmx_molblock_t>*, bool*, bool, bool, bool, warninp*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topio.cpp:135:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
135 | pairs->interactionTypes.emplace_back(InteractionOfType(atomNumbers, forceParam));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topio.cpp:135:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topio.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topio.cpp:39:
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp: In function 'void generate_LJCpairsNB(MoleculeInformation*, int, InteractionsOfType*, warninp*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:2658:71: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
2658 | add_param_to_list(&mol->interactions[F_LJC_PAIRS_NB], InteractionOfType(atoms, forceParam));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:2658:71: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp: In function 'void push_at(t_symtab*, PreprocessingAtomTypes*, PreprocessingBondAtomType*, char*, int, t_nbparam***, t_nbparam***, warninp*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:541:57: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
541 | InteractionOfType interactionType({}, forceParam, "");
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:541:57: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.cpp:40:
/usr/include/c++/9/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator) [with _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]':
/usr/include/c++/9/bits/vector.tcc:171:5: note: parameter passing for argument of type 'std::vector<InteractionOfType>::iterator' {aka '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >'} changed in GCC 7.1
171 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp: In function 'void push_vsitesn(Directive, gmx::ArrayRef<InteractionsOfType>, t_atoms*, char*, warninp*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:2443:41: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
2443 | add_param_to_list(&bond[ftype], InteractionOfType(atoms, forceParam));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:2443:41: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.cpp: In function 'void make_shake(gmx::ArrayRef<InteractionsOfType>, t_atoms*, int)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.cpp:162:59: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
162 | InteractionOfType(atomNumbers, forceParm));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.cpp:162:59: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.cpp:40:
/usr/include/c++/9/bits/stl_vector.h:1428:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1428 | { return _M_erase(begin() + (__position - cbegin())); }
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.cpp:194:63: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
194 | add_param_to_list(&(plist[F_CONSTR]), InteractionOfType(atomNumbers, forceParm));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.cpp:194:63: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.cpp:40:
/usr/include/c++/9/bits/stl_vector.h:1428:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1428 | { return _M_erase(begin() + (__position - cbegin())); }
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp: In function 'int add_atomtype_decoupled(t_symtab*, PreprocessingAtomTypes*, t_nbparam***, t_nbparam***)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:2574:49: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
2574 | nr = at->addType(symtab, atom, "decoupled", InteractionOfType({}, forceParam, ""), -1, 0);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:2574:49: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp: In function 'void generate_nbparams(int, int, InteractionsOfType*, PreprocessingAtomTypes*, warninp*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:103:73: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
103 | interactions->interactionTypes.emplace_back(InteractionOfType({}, forceParam));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:103:73: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:127:73: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
127 | interactions->interactionTypes.emplace_back(InteractionOfType({}, forceParam));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:127:73: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:151:73: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
151 | interactions->interactionTypes.emplace_back(InteractionOfType({}, forceParam));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:151:73: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:184:65: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
184 | interactions->interactionTypes.emplace_back(InteractionOfType({}, forceParam));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:184:65: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/toputil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toputil.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp: In function 'void push_bond(Directive, gmx::ArrayRef<InteractionsOfType>, gmx::ArrayRef<InteractionsOfType>, t_atoms*, PreprocessingAtomTypes*, char*, bool, bool, real, bool, bool*, warninp*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:1984:50: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1984 | InteractionOfType param(atoms, forceParam, "");
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:1984:50: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp: In function 'void push_cmap(Directive, gmx::ArrayRef<InteractionsOfType>, gmx::ArrayRef<InteractionsOfType>, t_atoms*, PreprocessingAtomTypes*, char*, warninp*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:2336:64: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
2336 | InteractionOfType param(atoms, forceParam, "");
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:2336:64: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toputil.cpp: In function 'void print_bondeds(FILE*, int, Directive, int, int, gmx::ArrayRef<const InteractionsOfType>)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toputil.cpp:340:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
340 | atype.addType(&stab, *a, buf, InteractionOfType({}, {}), 0, 0);
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toputil.cpp:340:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp: In function 'void push_bondtype(InteractionsOfType*, const InteractionOfType&, int, int, bool, const char*, warninp*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:711:17: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
711 | InteractionOfType(b.atoms(), b.forceParam(), b.interactionTypeName()));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:711:17: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:730:43: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
730 | bt->interactionTypes.emplace_back(InteractionOfType(atoms, forceParam, b.interactionTypeName()));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:730:43: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toputil.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toputil.cpp:39:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const InteractionOfType&}; _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<InteractionOfType>::iterator' {aka '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In function 'void add_param_to_list(InteractionsOfType*, const InteractionOfType&)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp: In function 'void push_bt(Directive, gmx::ArrayRef<InteractionsOfType>, int, PreprocessingAtomTypes*, PreprocessingBondAtomType*, char*, warninp*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:851:33: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
851 | push_bondtype(&(bt[ftype]), InteractionOfType(atomTypes, forceParam), nral, ftype, FALSE, line, wi);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:851:33: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/vsite_parm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp: In function 'void push_dihedraltype(Directive, gmx::ArrayRef<InteractionsOfType>, PreprocessingBondAtomType*, char*, warninp*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:1019:33: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1019 | push_bondtype(&(bt[ftype]), InteractionOfType(atoms, forceParam), 4, ftype, bAllowRepeat, line, wi);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:1019:33: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:39:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In function 'void push_cmaptype(Directive, gmx::ArrayRef<InteractionsOfType>, int, PreprocessingAtomTypes*, PreprocessingBondAtomType*, char*, warninp*)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:1286:33: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1286 | push_bondtype(&(bt[ftype]), InteractionOfType(atomTypes, forceParam), nral, ftype, FALSE, line, wi);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:1286:33: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/x2top.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/x2top.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:39:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const InteractionOfType&}; _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<InteractionOfType>::iterator' {aka '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In function 'void convert_moltype_couple(MoleculeInformation*, int, real, int, int, bool, int, InteractionsOfType*, warninp*)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:2606:31: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
2606 | paramnew.emplace_back(InteractionOfType(param.atoms(), forceParam, ""));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:2606:31: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp: In function 'bool calc_vsite4fdn_param(InteractionOfType*, gmx::ArrayRef<const VsiteBondedInteraction>, gmx::ArrayRef<const VsiteBondedInteraction>)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp:696:13: note: parameter passing for argument of type 'gmx::ArrayRef<const VsiteBondedInteraction>' changed in GCC 7.1
696 | static bool calc_vsite4fdn_param(InteractionOfType* vsite,
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp:696:13: note: parameter passing for argument of type 'gmx::ArrayRef<const VsiteBondedInteraction>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp: In function 'bool calc_vsite4fd_param(InteractionOfType*, gmx::ArrayRef<const VsiteBondedInteraction>, gmx::ArrayRef<const VsiteBondedInteraction>)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp:639:13: note: parameter passing for argument of type 'gmx::ArrayRef<const VsiteBondedInteraction>' changed in GCC 7.1
639 | static bool calc_vsite4fd_param(InteractionOfType* vsite,
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp:639:13: note: parameter passing for argument of type 'gmx::ArrayRef<const VsiteBondedInteraction>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/x2top.cpp: In function 'void lo_set_force_const(InteractionsOfType*, real*, int, bool, bool, bool)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/x2top.cpp:239:17: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
239 | param = InteractionOfType(param.atoms(), forceParam);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/x2top.cpp:239:17: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp:39:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {VsiteBondedInteraction}; _Tp = VsiteBondedInteraction; _Alloc = std::allocator<VsiteBondedInteraction>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<VsiteBondedInteraction>::iterator' {aka '__gnu_cxx::__normal_iterator<VsiteBondedInteraction*, std::vector<VsiteBondedInteraction> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/xlate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/xlate.cpp
/usr/include/c++/9/bits/vector.tcc: In function 'void enter_bonded(int, std::vector<VsiteBondedInteraction>*, const InteractionOfType&)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<VsiteBondedInteraction*, std::vector<VsiteBondedInteraction> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/x2top.cpp: In function 'int gmx_x2top(int, char**)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/x2top.cpp:137:41: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
137 | add_param_to_list(bond, InteractionOfType(atoms, forceParam));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/x2top.cpp:137:41: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/x2top.cpp:239:17: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
239 | param = InteractionOfType(param.atoms(), forceParam);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/x2top.cpp:239:17: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp: In function 'int set_vsites(bool, t_atoms*, PreprocessingAtomTypes*, gmx::ArrayRef<InteractionsOfType>)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp:837:57: note: parameter passing for argument of type 'gmx::ArrayRef<const VsiteBondedInteraction>' changed in GCC 7.1
837 | bERROR = calc_vsite4fd_param(¶m, allVsiteBondeds.bonds,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
838 | allVsiteBondeds.angles);
| ~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp:837:57: note: parameter passing for argument of type 'gmx::ArrayRef<const VsiteBondedInteraction>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp:837:57: note: parameter passing for argument of type 'gmx::ArrayRef<const VsiteBondedInteraction>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp:841:58: note: parameter passing for argument of type 'gmx::ArrayRef<const VsiteBondedInteraction>' changed in GCC 7.1
841 | bERROR = calc_vsite4fdn_param(¶m, allVsiteBondeds.bonds,
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
842 | allVsiteBondeds.angles);
| ~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp:841:58: note: parameter passing for argument of type 'gmx::ArrayRef<const VsiteBondedInteraction>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp:841:58: note: parameter passing for argument of type 'gmx::ArrayRef<const VsiteBondedInteraction>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/correlationfunctions/autocorr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/autocorr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/correlationfunctions/crosscorr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/crosscorr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/correlationfunctions/expfit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/expfit.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp:39:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {InteractionOfType&}; _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<InteractionOfType>::iterator' {aka '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/autocorr.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/autocorr.cpp:46:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/autocorr.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/autocorr.cpp:46:
/usr/include/c++/9/bits/stl_vector.h: In function 'void low_do_four_core(int, real*, real*, int)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator) [with _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]':
/usr/include/c++/9/bits/vector.tcc:171:5: note: parameter passing for argument of type 'std::vector<InteractionOfType>::iterator' {aka '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >'} changed in GCC 7.1
171 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In function 'void low_do_autocorr(const char*, const gmx_output_env_t*, const char*, int, int, int, real**, real, long unsigned int, int, gmx_bool, gmx_bool, gmx_bool, real, real, int)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In function 'void clean_vsite_bondeds(gmx::ArrayRef<InteractionsOfType>, int, bool)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp:39:
/usr/include/c++/9/bits/stl_vector.h:1428:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1428 | { return _M_erase(begin() + (__position - cbegin())); }
| ^
/usr/include/c++/9/bits/stl_vector.h:1428:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1428 | { return _M_erase(begin() + (__position - cbegin())); }
| ^
/usr/include/c++/9/bits/stl_vector.h:1428:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1428 | { return _M_erase(begin() + (__position - cbegin())); }
| ^
/usr/include/c++/9/bits/stl_vector.h:1428:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1428 | { return _M_erase(begin() + (__position - cbegin())); }
| ^
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/correlationfunctions/gmx_lmcurve.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/gmx_lmcurve.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/correlationfunctions/integrate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/integrate.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/correlationfunctions/manyautocorrelation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/manyautocorrelation.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/correlationfunctions/polynomials.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/polynomials.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/statistics/statistics.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/statistics/statistics.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/manyautocorrelation.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/manyautocorrelation.cpp:44:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/abstractdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/abstractdata.cpp
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/manyautocorrelation.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/manyautocorrelation.cpp:44:
/usr/include/c++/9/bits/stl_vector.h: In function '_Z16many_auto_correlPSt6vectorIS_IdSaIdEESaIS1_EE._omp_fn.0':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In function 'int many_auto_correl(std::vector<std::vector<double> >*)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/analysisdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/analysisdata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/arraydata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/arraydata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/dataframe.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/dataframe.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/datamodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datamodule.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/datamodulemanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datamodulemanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/dataproxy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/dataproxy.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/arraydata.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/arraydata.cpp:44:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In constructor 'gmx::AbstractAnalysisArrayData::AbstractAnalysisArrayData()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/datastorage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/modules/average.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/average.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/modules/displacement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/displacement.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/modules/frameaverager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/frameaverager.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp:44:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const gmx::AnalysisDataValue&}; _Tp = gmx::AnalysisDataValue; _Alloc = std::allocator<gmx::AnalysisDataValue>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::AnalysisDataValue>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::AnalysisDataValue*, std::vector<gmx::AnalysisDataValue> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::AnalysisDataValue>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::AnalysisDataValue*, std::vector<gmx::AnalysisDataValue> >'} changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/modules/histogram.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/histogram.cpp
/<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp: In member function 'void gmx::internal::AnalysisDataStorageFrameData::addPointSet(int, int, gmx::ArrayRef<const gmx::AnalysisDataValue>)':
/<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp:583:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::AnalysisDataValue>' changed in GCC 7.1
583 | void AnalysisDataStorageFrameData::addPointSet(int dataSetIndex,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp:44:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::AnalysisDataValue*, std::vector<gmx::AnalysisDataValue> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp: In member function 'void gmx::AnalysisDataStorageFrame::finishPointSet()':
/<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp:714:27: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::AnalysisDataValue>' changed in GCC 7.1
714 | data_->addPointSet(currentDataSet_, firstColumn,
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
715 | makeConstArrayRef(values_).subArray(begin, end - begin));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp:714:27: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::AnalysisDataValue>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/modules/lifetime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/lifetime.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/modules/plot.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/plot.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/coordinateio/coordinatefile.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/coordinatefile.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/coordinateio/outputadaptercontainer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadaptercontainer.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/outputselector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/outputselector.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setatoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/setatoms.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setforces.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/setforces.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setprecision.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/setprecision.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setstarttime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/setstarttime.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/settimestep.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/settimestep.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setvelocities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/setvelocities.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/coordinateio/requirements.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/requirements.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/analysismodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysismodule.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/analysissettings.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysissettings.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/cmdlinerunner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/cmdlinerunner.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/angle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/angle.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/convert_trj.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/convert_trj.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/distance.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/distance.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/extract_cluster.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/extract_cluster.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/freevolume.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/pairdist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/pairdist.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/rdf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/rdf.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysismodule.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.cpp:44:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysismodule.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.cpp:44:
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual void gmx::analysismodules::{anonymous}::FreeVolume::initAnalysis(const gmx::TrajectoryAnalysisSettings&, const gmx::TopologyInformation&)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysismodule.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.cpp:44:
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/sasa.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/sasa.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/select.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/select.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysismodule.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/sasa.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/sasa.cpp:46:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/surfacearea.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.cpp
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysismodule.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/sasa.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/sasa.cpp:46:
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual void gmx::analysismodules::{anonymous}::Sasa::initAnalysis(const gmx::TrajectoryAnalysisSettings&, const gmx::TopologyInformation&)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/trajectory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/trajectory.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/runnercommon.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/runnercommon.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/topologyinformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/topologyinformation.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tools/check.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/check.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tools/convert_tpr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/convert_tpr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tools/dump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/dump.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tools/eneconv.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/eneconv.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tools/make_ndx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/make_ndx.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tools/mk_angndx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/mk_angndx.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tools/pme_error.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/pme_error.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tools/report_methods.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/report_methods.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tools/trjcat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/trjcat.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tools/trjconv.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/trjconv.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tools/tune_pme.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/tune_pme.cpp
/<<PKGBUILDDIR>>/src/gromacs/tools/trjconv.cpp: In function 'int gmx_trjconv(int, char**)':
/<<PKGBUILDDIR>>/src/gromacs/tools/trjconv.cpp:1245:66: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1245 | put_atoms_in_compact_unitcell(ePBC, ecenter, fr.box, positionsArrayRef);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tools/trjconv.cpp:1245:66: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxlib/conformation_utilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/conformation_utilities.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxlib/network.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/network.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxlib/nrnb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nrnb.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_free_energy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_free_energy.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/boxdeformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/boxdeformation.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/boxdeformation.cpp: In member function 'void gmx::BoxDeformation::apply(gmx::ArrayRef<gmx::BasicVector<double> >, real (*)[3], int64_t)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/boxdeformation.cpp:106:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
106 | void BoxDeformation::apply(ArrayRef<RVec> x, matrix box, int64_t step)
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/broadcaststructs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.cpp:40:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/calc_verletbuf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/calc_verletbuf.cpp
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.cpp:40:
/usr/include/c++/9/bits/stl_vector.h: In function 'void broadcastStateWithoutDynamics(const t_commrec*, t_state*)':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/calcmu.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/calcmu.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/calcmu.cpp: In function 'void calc_mu(int, int, gmx::ArrayRef<gmx::BasicVector<double> >, const real*, const real*, int, double*, double*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/calcmu.cpp:50:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
50 | void calc_mu(int start,
| ^~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/calcvir.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/calcvir.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/calc_verletbuf.h:39,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/calc_verletbuf.cpp:38:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {VerletbufAtomtype}; _Tp = VerletbufAtomtype; _Alloc = std::allocator<VerletbufAtomtype>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<VerletbufAtomtype>::iterator' {aka '__gnu_cxx::__normal_iterator<VerletbufAtomtype*, std::vector<VerletbufAtomtype> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In function 'std::vector<VerletbufAtomtype> getVerletBufferAtomtypes(const gmx_mtop_t&, bool)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<VerletbufAtomtype*, std::vector<VerletbufAtomtype> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/checkpointhandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/checkpointhandler.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/compute_io.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/compute_io.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/constr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/constraintrange.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp: In function 'void gmx::constr_recur(const t_blocka*, const InteractionLists&, gmx::ArrayRef<const t_iparams>, gmx_bool, int, int, int, int*, real, real, real*, int*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp:60:13: note: parameter passing for argument of type 'gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
60 | static void constr_recur(const t_blocka* at2con,
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp: In function 'void gmx::constr_recur(const t_blocka*, const InteractionLists&, gmx::ArrayRef<const t_iparams>, gmx_bool, int, int, int, int*, real, real, real*, int*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp:60:13: note: parameter passing for argument of type 'gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/coupling.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp: In function 't_blocka gmx::make_at2con(const gmx_moltype_t&, gmx::ArrayRef<const t_iparams>, gmx::FlexibleConstraintTreatment)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp:826:10: note: parameter passing for argument of type 'gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
826 | t_blocka make_at2con(const gmx_moltype_t& moltype,
| ^~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/dispersioncorrection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp: In constructor 'DispersionCorrection::TopologyParams::TopologyParams(const gmx_mtop_t&, const t_inputrec&, bool, int, gmx::ArrayRef<const double>)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp:107:1: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
107 | DispersionCorrection::TopologyParams::TopologyParams(const gmx_mtop_t& mtop,
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp: In constructor 'DispersionCorrection::DispersionCorrection(const gmx_mtop_t&, const t_inputrec&, bool, int, gmx::ArrayRef<const double>, const interaction_const_t&, const char*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp:520:1: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
520 | DispersionCorrection::DispersionCorrection(const gmx_mtop_t& mtop,
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp:530:85: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
530 | topParams_(mtop, inputrec, useBuckingham, numAtomTypes, nonbondedForceParameters)
| ^
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/ebin.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp: In function 'void andersen_tcoupl(const t_inputrec*, int64_t, const t_commrec*, const t_mdatoms*, gmx::ArrayRef<gmx::BasicVector<double> >, real, const std::vector<bool>&, gmx::ArrayRef<const double>)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp:810:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
810 | void andersen_tcoupl(const t_inputrec* ir,
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp:810:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/enerdata_utils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/ebin.cpp: In function 'void add_ebin_indexed(t_ebin*, int, gmx::ArrayRef<bool>, gmx::ArrayRef<const double>, gmx_bool)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/ebin.cpp:197:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
197 | void add_ebin_indexed(t_ebin* eb,
| ^~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/energyoutput.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/energyoutput.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/expanded.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp: In function 'void sum_dhdl(gmx_enerdata_t*, gmx::ArrayRef<const double>, const t_lambda&)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp:92:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
92 | void sum_dhdl(gmx_enerdata_t* enerd, gmx::ArrayRef<const real> lambda, const t_lambda& fepvals)
| ^~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/force.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp: In function 'void do_force_lowlevel(t_forcerec*, const t_inputrec*, const t_idef*, const t_commrec*, const gmx_multisim_t*, t_nrnb*, gmx_wallcycle_t, const t_mdatoms*, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, history_t*, gmx::ForceOutputs*, gmx_enerdata_t*, t_fcdata*, const real (*)[3], const real*, const t_graph*, const real (*)[3], const gmx::StepWorkload&, const DDBalanceRegionHandler&)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp:290:40: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
290 | status = gmx_pme_do(
| ~~~~~~~~~~^
291 | fr->pmedata,
| ~~~~~~~~~~~~
292 | gmx::constArrayRefFromArray(coordinates.unpaddedConstArrayRef().data(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
293 | md->homenr - fr->n_tpi),
| ~~~~~~~~~~~~~~~~~~~~~~~~
294 | forceWithVirial.force_, md->chargeA, md->chargeB, md->sqrt_c6A,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
295 | md->sqrt_c6B, md->sigmaA, md->sigmaB, box, cr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
296 | DOMAINDECOMP(cr) ? dd_pme_maxshift_x(cr->dd) : 0,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
297 | DOMAINDECOMP(cr) ? dd_pme_maxshift_y(cr->dd) : 0, nrnb, wcycle,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
298 | ewaldOutput.vir_q, ewaldOutput.vir_lj, &Vlr_q, &Vlr_lj,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
299 | lambda[efptCOUL], lambda[efptVDW], &ewaldOutput.dvdl[efptCOUL],
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
300 | &ewaldOutput.dvdl[efptVDW], pme_flags);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp:290:40: note: parameter passing for argument of type 'const gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp:290:40: note: parameter passing for argument of type 'const gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp:325:40: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
325 | gmx_pme_calc_energy(
| ~~~~~~~~~~~~~~~~~~~^
326 | fr->pmedata,
| ~~~~~~~~~~~~
327 | coordinates.unpaddedConstArrayRef().subArray(md->homenr - fr->n_tpi, fr->n_tpi),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
328 | gmx::arrayRefFromArray(md->chargeA + md->homenr - fr->n_tpi, fr->n_tpi),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
329 | &Vlr_q);
| ~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp:325:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp:325:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/forcerec.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/energyoutput.cpp: In member function 'void gmx::EnergyOutput::addDataAtEnergyStep(bool, bool, double, real, const gmx_enerdata_t*, const t_state*, const t_lambda*, const t_expanded*, const real (*)[3], const real (*)[3], const real (*)[3], const real (*)[3], const real (*)[3], const gmx_ekindata_t*, const real*, const gmx::Constraints*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/energyoutput.cpp:881:21: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
881 | add_ebin_indexed(ebin_, ie_, gmx::ArrayRef<bool>(bEner_), enerd->term, bSum);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/gmx_omp_nthreads.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/groupcoord.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp
In file included from /usr/include/c++/9/memory:80,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.h:40,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/forcerec.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/forcerec.cpp:39:
/usr/include/c++/9/bits/unique_ptr.h: In function 'void init_forcerec(FILE*, const gmx::MDLogger&, t_forcerec*, t_fcdata*, const t_inputrec*, const gmx_mtop_t*, const t_commrec*, real (*)[3], const char*, const char*, gmx::ArrayRef<const std::__cxx11::basic_string<char> >, const gmx_hw_info_t&, const gmx_device_info_t*, bool, bool, real, gmx_wallcycle*)':
/usr/include/c++/9/bits/unique_ptr.h:857:30: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
857 | { return unique_ptr<_Tp>(new _Tp(std::forward<_Args>(__args)...)); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/md_support.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/md_support.cpp: In function 'void setCurrentLambdasLocal(int64_t, const t_lambda*, const double*, gmx::ArrayRef<double>, int)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/md_support.cpp:356:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
356 | void setCurrentLambdasLocal(const int64_t step,
| ^~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdebin_bar.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.cpp:39:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::HostAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.cpp:39:
/usr/include/c++/9/bits/stl_vector.h: In function 'void gmx::changePinningPolicy(PinnableVector*, gmx::PinningPolicy) [with PinnableVector = gmx::PaddedVector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> >]':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'void gmx::MDAtoms::resize(int)':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:46:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/membed.cpp
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:46:
/usr/include/c++/9/bits/stl_vector.h: In function 'void gmx::set_lincs(const t_idef&, const t_mdatoms&, bool, const t_commrec*, gmx::Lincs*)':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp: In function 'void mdoutf_write_to_trajectory_files(FILE*, const t_commrec*, gmx_mdoutf_t, int, int, int64_t, double, t_state*, t_state*, ObservablesHistory*, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp:257:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
257 | void mdoutf_write_to_trajectory_files(FILE* fplog,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp:282:31: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
282 | dd_collect_vec(cr->dd, state_local, state_local->x, globalXRef);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp:287:31: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
287 | dd_collect_vec(cr->dd, state_local, state_local->v, globalVRef);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp:293:27: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
293 | dd_collect_vec(cr->dd, state_local, f_local,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
294 | gmx::arrayRefFromArray(reinterpret_cast<gmx::RVec*>(f_global), f_local.size()));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/nsgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nsgrid.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/perf_est.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qm_gamess.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_gamess.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qm_gaussian.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_gaussian.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qm_mopac.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_mopac.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qm_orca.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_orca.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qmmm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qmmm.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/resethandler.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp: In function 'int add_binr(t_bin*, gmx::ArrayRef<const double>)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp:103:5: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
103 | int add_binr(t_bin* b, gmx::ArrayRef<const real> r)
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp:103:5: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp: In function 'void extract_binr(t_bin*, int, gmx::ArrayRef<double>)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp:160:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
160 | void extract_binr(t_bin* b, int index, gmx::ArrayRef<real> r)
| ^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/rf_util.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/settle.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/sighandler.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/simulationsignal.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/splitter.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp: In function 'void do_force(FILE*, const t_commrec*, const gmx_multisim_t*, const t_inputrec*, gmx::Awh*, gmx_enfrot*, gmx::ImdSession*, pull_t*, int64_t, t_nrnb*, gmx_wallcycle_t, const gmx_localtop_t*, const real (*)[3], gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, history_t*, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, real (*)[3], const t_mdatoms*, gmx_enerdata_t*, t_fcdata*, gmx::ArrayRef<double>, t_graph*, t_forcerec*, gmx::MdrunScheduleWorkload*, const gmx_vsite_t*, real*, double, gmx_edsam*, int, const DDBalanceRegionHandler&)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:895:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
895 | void do_force(FILE* fplog,
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1070:43: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1070 | stateGpu->copyCoordinatesToGpu(x.unpaddedArrayRef(), AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1103:41: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1103 | stateGpu->copyCoordinatesFromGpu(x.unpaddedArrayRef(), AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1154:30: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1154 | nbnxn_put_on_grid(nbv, box, 0, vzero, box_diag, nullptr, { 0, mdatoms->homenr }, -1,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1155 | fr->cginfo, x.unpaddedArrayRef(), 0, nullptr);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1161:39: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1161 | nbnxn_put_on_grid_nonlocal(nbv, domdec_zones(cr->dd), fr->cginfo, x.unpaddedArrayRef());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1243:36: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1243 | nbv->convertCoordinates(AtomLocality::Local, false, x.unpaddedArrayRef());
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1243:36: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1320:53: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1320 | stateGpu->copyCoordinatesFromGpu(x.unpaddedArrayRef(), AtomLocality::NonLocal);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1337:51: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1337 | stateGpu->copyCoordinatesToGpu(x.unpaddedArrayRef(), AtomLocality::NonLocal);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1345:40: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1345 | nbv->convertCoordinates(AtomLocality::NonLocal, false, x.unpaddedArrayRef());
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1345:40: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1525:53: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1525 | nbnxn_atomdata_add_nbat_fshift_to_fshift(*nbv->nbat,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
1526 | forceOut.forceWithShiftForces().shiftForces());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1589:46: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1589 | stateGpu->copyForcesToGpu(forceOut.forceWithShiftForces().force(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1590 | AtomLocality::NonLocal);
| ~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1601:48: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1601 | stateGpu->copyForcesFromGpu(forceOut.forceWithShiftForces().force(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1602 | AtomLocality::NonLocal);
| ~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1613:57: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1613 | nbnxn_atomdata_add_nbat_fshift_to_fshift(*nbv->nbat, forceWithShiftForces.shiftForces());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1634:46: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1634 | stateGpu->copyForcesToGpu(forceOut.forceWithShiftForces().force(), AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1771:42: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1771 | stateGpu->copyForcesToGpu(forceWithShift, locality);
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1790:44: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1790 | stateGpu->copyForcesFromGpu(forceWithShift, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/stat.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/stophandler.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tgroup.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/trajectory_writing.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/update.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/update_constrain_cuda_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/update_constrain_cuda_impl.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/trajectory_writing.cpp: In function 'void do_md_trajectory_writing(FILE*, t_commrec*, int, const t_filenm*, int64_t, int64_t, double, t_inputrec*, t_state*, t_state*, ObservablesHistory*, const gmx_mtop_t*, t_forcerec*, gmx_mdoutf_t, const gmx::EnergyOutput&, gmx_ekindata_t*, gmx::ArrayRef<gmx::BasicVector<double> >, gmx_bool, gmx_bool, gmx_bool, gmx_bool, gmx_bool)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/trajectory_writing.cpp:56:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
56 | void do_md_trajectory_writing(FILE* fplog,
| ^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/trajectory_writing.cpp:165:41: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
165 | mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, top_global->natoms, step, t,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
166 | state, state_global, observablesHistory, f);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroups.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update_constrain_cuda_impl.cpp: In member function 'void gmx::UpdateConstrainCuda::integrate(GpuEventSynchronizer*, real, bool, bool, real (*)[3], bool, gmx::ArrayRef<const t_grp_tcstat>, bool, float, const real (*)[3])':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update_constrain_cuda_impl.cpp:70:6: note: parameter passing for argument of type 'gmx::ArrayRef<const t_grp_tcstat>' changed in GCC 7.1
70 | void UpdateConstrainCuda::integrate(GpuEventSynchronizer* /* fReadyOnDevice */,
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp:45:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const gmx::BasicVector<double>&}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp: In function 'void update_pcouple_after_coordinates(FILE*, int64_t, const t_inputrec*, const t_mdatoms*, const real (*)[3], const real (*)[3], const real (*)[3], real (*)[3], t_state*, t_nrnb*, gmx::Update*, bool)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp:1752:29: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1752 | upd->deform()->apply(localX, state->box, step);
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp: In function 'gmx_bool update_randomize_velocities(const t_inputrec*, int64_t, const t_commrec*, const t_mdatoms*, gmx::ArrayRef<gmx::BasicVector<double> >, const gmx::Update*, const gmx::Constraints*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp:1868:17: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1868 | extern gmx_bool update_randomize_velocities(const t_inputrec* ir,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp:1896:24: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1896 | andersen_tcoupl(ir, step, cr, md, v, rate, upd->sd()->randomize_group, upd->sd()->boltzfac);
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp:1896:24: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp: In member function 'void gmx::UpdateGroupsCog::addCogs(gmx::ArrayRef<const int>, gmx::ArrayRef<const gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp:80:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
80 | void UpdateGroupsCog::addCogs(gmx::ArrayRef<const int> globalAtomIndices,
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp:45:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.h:40,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp:39:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/vcm.cpp
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.h:40,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp:39:
/usr/include/c++/9/bits/stl_vector.h: In member function 'void gmx::Update::setNumAtoms(int)':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In constructor 'gmx::Update::Impl::Impl(const t_inputrec*, gmx::BoxDeformation*)':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/wall.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfittingamplitudelookup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingamplitudelookup.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp: In function 'void constructVsitesGlobal(const gmx_mtop_t&, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:741:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
741 | void constructVsitesGlobal(const gmx_mtop_t& mtop, gmx::ArrayRef<gmx::RVec> x)
| ^~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:741:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingamplitudelookup.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingamplitudelookup.cpp:44:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingamplitudelookup.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingamplitudelookup.cpp:44:
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual const std::vector<double>& gmx::{anonymous}::UnitAmplitudes::operator()(const t_mdatoms&, gmx::ArrayRef<const int>)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfittingforceprovider.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingforceprovider.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/topology/idef.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:39:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/topology/idef.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:39:
/usr/include/c++/9/bits/stl_vector.h: In function '_Z25split_vsites_over_threadsPK7t_ilistPK9t_iparamsPK9t_mdatomsP11gmx_vsite_t._omp_fn.0':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingforceprovider.cpp: In constructor 'gmx::DensityFittingForceProvider::Impl::Impl(const gmx::DensityFittingParameters&, gmx::basic_mdspan<const float, gmx::extents<-1, -1, -1> >, const gmx::TranslateAndScale&, const gmx::LocalAtomSet&, int, double, const gmx::DensityFittingForceProviderState&)':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingforceprovider.cpp:79:19: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
79 | scaleToLattice({ &sigmaInLatticeCoordinates, &sigmaInLatticeCoordinates + 1 });
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingforceprovider.cpp:166:82: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
166 | transformationToDensityLattice_.scaleOperationOnly().inverseIgnoringZeroScale(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
167 | { &referenceDensityCenter_, &referenceDensityCenter_ + 1 });
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingforceprovider.cpp:171:36: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
171 | transformationToDensityLattice_({ &referenceDensityOriginShift, &referenceDensityOriginShift + 1 });
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingforceprovider.cpp:172:82: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
172 | transformationToDensityLattice_.scaleOperationOnly().inverseIgnoringZeroScale(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
173 | { &referenceDensityOriginShift, &referenceDensityOriginShift + 1 });
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingforceprovider.cpp: In member function 'void gmx::DensityFittingForceProvider::Impl::calculateForces(const gmx::ForceProviderInput&, gmx::ForceProviderOutput*)':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingforceprovider.cpp:210:36: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
210 | transformationToDensityLattice_(transformedCoordinates_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingforceprovider.cpp:258:82: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
258 | transformationToDensityLattice_.scaleOperationOnly().inverseIgnoringZeroScale(forces_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfittingoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingoptions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfittingoutputprovider.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingoutputprovider.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfittingparameters.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingparameters.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/electricfield.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/electricfield.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/bonded.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/bonded.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/disre.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/disre.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/gpubonded_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/gpubonded_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/listed_forces.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/listed_forces.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/listed_internal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/listed_internal.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/manage_threading.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/manage_threading.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/orires.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/orires.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/pairs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/pairs.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/position_restraints.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/position_restraints.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/restcbt.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/restcbt.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/calculate_spline_moduli.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/calculate_spline_moduli.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/ewald.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/ewald.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/ewald_utils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/ewald_utils.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/long_range_correction.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/long_range_correction.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_gather.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_gather.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_grid.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_load_balancing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_only.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/forcerec.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp:47:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const pme_setup_t&}; _Tp = pme_setup_t; _Alloc = std::allocator<pme_setup_t>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pme_setup_t>::iterator' {aka '__gnu_cxx::__normal_iterator<pme_setup_t*, std::vector<pme_setup_t> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp: In function 'void pme_load_balance(pme_load_balancing_t*, t_commrec*, FILE*, FILE*, const gmx::MDLogger&, const t_inputrec&, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, double, interaction_const_t*, nonbonded_verlet_t*, gmx_pme_t**, int64_t)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp:551:13: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
551 | static void pme_load_balance(pme_load_balancing_t* pme_lb,
| ^~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/forcerec.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp:47:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pme_setup_t*, std::vector<pme_setup_t> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp: In function 'void pme_loadbal_do(pme_load_balancing_t*, t_commrec*, FILE*, FILE*, const gmx::MDLogger&, const t_inputrec&, t_forcerec*, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, gmx_wallcycle_t, int64_t, int64_t, gmx_bool*, bool)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp:896:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
896 | void pme_loadbal_do(pme_load_balancing_t* pme_lb,
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp:1035:25: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1035 | pme_load_balance(pme_lb, cr, fp_err, fp_log, mdlog, ir, box, x,
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1036 | pme_lb->cycles_c - cycles_prev, fr->ic, fr->nbv.get(), &fr->pmedata, step);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp: In function 'void gmx_pme_calc_energy(gmx_pme_t*, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<const double>, real*)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:952:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
952 | void gmx_pme_calc_energy(gmx_pme_t* pme, gmx::ArrayRef<const gmx::RVec> x, gmx::ArrayRef<const real> q, real* V)
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:952:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_pp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_pp.cpp
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp: In function 'int gmx_pme_do(gmx_pme_t*, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >, real*, real*, real*, real*, real*, real*, const real (*)[3], const t_commrec*, int, int, t_nrnb*, gmx_wallcycle*, real (*)[3], real (*)[3], real*, real*, real, real, real*, real*, int)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1004:5: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1004 | int gmx_pme_do(struct gmx_pme_t* pme,
| ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1004:5: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1154:33: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1154 | do_redist_pos_coeffs(pme, cr, bFirst, coordinates, coefficient);
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1154:33: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1384:37: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1384 | do_redist_pos_coeffs(pme, cr, bFirst, coordinates, RedistC6);
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1384:37: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1393:37: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1393 | do_redist_pos_coeffs(pme, cr, FALSE, coordinates, RedistSigma);
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1393:37: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp:72:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::HostAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp:72:
/usr/include/c++/9/bits/stl_vector.h: In function 'void gmx::changePinningPolicy(PinnableVector*, gmx::PinningPolicy) [with PinnableVector = gmx::PaddedVector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> >]':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_redistribute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_redistribute.cpp
/usr/include/c++/9/bits/stl_vector.h: In function 'int gmx_pmeonly(gmx_pme_t*, const t_commrec*, t_nrnb*, gmx_wallcycle*, gmx_walltime_accounting_t, t_inputrec*, PmeRunMode)':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp:711:47: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
711 | stateGpu->copyCoordinatesToGpu(gmx::ArrayRef<gmx::RVec>(pme_pp->x), gmx::AtomLocality::All);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp:728:23: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
728 | gmx_pme_do(pme, pme_pp->x, pme_pp->f, pme_pp->chargeA.data(), pme_pp->chargeB.data(),
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
729 | pme_pp->sqrt_c6A.data(), pme_pp->sqrt_c6B.data(), pme_pp->sigmaA.data(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
730 | pme_pp->sigmaB.data(), box, cr, maxshift_x, maxshift_y, mynrnb, wcycle,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
731 | output.coulombVirial_, output.lennardJonesVirial_, &output.coulombEnergy_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
732 | &output.lennardJonesEnergy_, lambda_q, lambda_lj, &dvdlambda_q,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
733 | &dvdlambda_lj, pmeFlags);
| ~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp:728:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp:728:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_solve.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_solve.cpp
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_redistribute.cpp: In function 'void dd_pmeredist_f(gmx_pme_t*, PmeAtomComm*, gmx::ArrayRef<gmx::BasicVector<double> >, gmx_bool)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_redistribute.cpp:388:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
388 | void dd_pmeredist_f(struct gmx_pme_t* pme, PmeAtomComm* atc, gmx::ArrayRef<gmx::RVec> f, gmx_bool bAddF)
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_spline_work.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_spline_work.cpp
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_redistribute.cpp: In function 'void do_redist_pos_coeffs(gmx_pme_t*, const t_commrec*, gmx_bool, gmx::ArrayRef<const gmx::BasicVector<double> >, const real*)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_redistribute.cpp:453:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
453 | void do_redist_pos_coeffs(struct gmx_pme_t* pme,
| ^~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_spread.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_spread.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_gpu_program.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/legacymdrunoptions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/legacysimulator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/md.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/mdmodules.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/mdmodules.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:53:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:54:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:54:
/usr/include/c++/9/bits/stl_vector.h: In function 'void gmx::changePinningPolicy(PinnableVector*, gmx::PinningPolicy) [with PinnableVector = gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >]':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp: In member function 'void gmx::LegacySimulator::do_mimic()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:227:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
227 | initialize_lambdas(fplog, *ir, MASTER(cr), &state_global->fep_state, state_global->lambda, lam0);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:53:
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:379:35: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
379 | setCurrentLambdasLocal(step, ir->fepvals, lam0, state->lambda, state->fep_state);
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:421:32: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
421 | relax_shell_flexcon(fplog, cr, ms, mdrunOptions.verbose, enforcedRotation, step, ir,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
422 | imdSession, pull_work, bNS, force_flags, &top, constr, enerd, fcd,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
423 | state->natoms, state->x.arrayRefWithPadding(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
424 | state->v.arrayRefWithPadding(), state->box, state->lambda, &state->hist,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
425 | f.arrayRefWithPadding(), force_vir, mdatoms, nrnb, wcycle, graph,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
426 | shellfc, fr, runScheduleWork, t, mu_tot, vsite, ddBalanceRegionHandler);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:437:21: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
437 | do_force(fplog, cr, ms, ir, awh, enforcedRotation, imdSession, pull_work, step, nrnb,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
438 | wcycle, &top, state->box, state->x.arrayRefWithPadding(), &state->hist,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
439 | f.arrayRefWithPadding(), force_vir, mdatoms, enerd, fcd, state->lambda, graph,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
440 | fr, runScheduleWork, vsite, mu_tot, t, ed, GMX_FORCE_NS | force_flags,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
441 | ddBalanceRegionHandler);
| ~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:451:37: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
451 | do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t, ir, state,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
452 | state_global, observablesHistory, top_global, fr, outf,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
453 | energyOutput, ekind, f, isCheckpointingStep, doRerun,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
454 | isLastStep, mdrunOptions.writeConfout, bSumEkinhOld);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:509:31: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
509 | dd_collect_vec(cr->dd, state, flocal, ftemp);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:519:45: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
519 | mimicCommunicator.sendForces(ftemp, state_global->natoms);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:533:21: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
533 | sum_dhdl(enerd, state->lambda, *ir->fepvals);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp: In member function 'void gmx::LegacySimulator::do_md()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:257:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
257 | initialize_lambdas(fplog, *ir, MASTER(cr), &state_global->fep_state, state_global->lambda, lam0);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:54:
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:762:49: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
762 | stateGpu->copyCoordinatesFromGpu(state->x, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:766:27: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
766 | pme_loadbal_do(pme_loadbal, cr, (mdrunOptions.verbose && MASTER(cr)) ? stderr : nullptr,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
767 | fplog, mdlog, *ir, fr, state->box, state->x, wcycle, step, step_rel,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
768 | &bPMETunePrinting, simulationWork.useGpuPmePpCommunication);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:780:35: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
780 | setCurrentLambdasLocal(step, ir->fepvals, lam0, state->lambda, state->fep_state);
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:823:44: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
823 | stateGpu->copyVelocitiesFromGpu(state->v, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:828:45: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
828 | stateGpu->copyCoordinatesFromGpu(state->x, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:931:32: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
931 | relax_shell_flexcon(fplog, cr, ms, mdrunOptions.verbose, enforcedRotation, step, ir,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
932 | imdSession, pull_work, bNS, force_flags, &top, constr, enerd, fcd,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
933 | state->natoms, state->x.arrayRefWithPadding(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
934 | state->v.arrayRefWithPadding(), state->box, state->lambda, &state->hist,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
935 | f.arrayRefWithPadding(), force_vir, mdatoms, nrnb, wcycle, graph,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
936 | shellfc, fr, runScheduleWork, t, mu_tot, vsite, ddBalanceRegionHandler);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:958:21: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
958 | do_force(fplog, cr, ms, ir, awh.get(), enforcedRotation, imdSession, pull_work, step,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
959 | nrnb, wcycle, &top, state->box, state->x.arrayRefWithPadding(), &state->hist,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
960 | f.arrayRefWithPadding(), force_vir, mdatoms, enerd, fcd, state->lambda, graph,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
961 | fr, runScheduleWork, vsite, mu_tot, t, ed ? ed->getLegacyED() : nullptr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
962 | (bNS ? GMX_FORCE_NS : 0) | force_flags, ddBalanceRegionHandler);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1113:25: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1113 | sum_dhdl(enerd, state->lambda, *ir->fepvals);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1141:45: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1141 | stateGpu->copyCoordinatesFromGpu(state->x, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1149:44: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1149 | stateGpu->copyVelocitiesFromGpu(state->v, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1165:40: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1165 | stateGpu->copyForcesFromGpu(ArrayRef<RVec>(f), AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1172:33: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1172 | do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t, ir, state, state_global,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1173 | observablesHistory, top_global, fr, outf, energyOutput, ekind, f,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1174 | checkpointHandler->isCheckpointingStep(), bRerunMD, bLastStep,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1175 | mdrunOptions.writeConfout, bSumEkinhOld);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1207:55: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1207 | bIfRandomize = update_randomize_velocities(ir, step, cr, mdatoms, state->v, &upd, constr);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1279:46: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1279 | stateGpu->copyVelocitiesToGpu(state->v, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1280:47: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1280 | stateGpu->copyCoordinatesToGpu(state->x, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1286:42: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1286 | stateGpu->copyForcesToGpu(ArrayRef<RVec>(f), AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1293:34: note: parameter passing for argument of type 'gmx::ArrayRef<const t_grp_tcstat>' changed in GCC 7.1
1293 | integrator->integrate(stateGpu->getForcesReadyOnDeviceEvent(
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1294 | AtomLocality::Local, runScheduleWork->stepWork.useGpuFBufferOps),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1295 | ir->delta_t, true, bCalcVir, shake_vir, doTemperatureScaling,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1296 | ekind->tcstat, doParrinelloRahman, ir->nstpcouple * ir->delta_t, M);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1303:48: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1303 | stateGpu->copyVelocitiesFromGpu(state->v, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1406:53: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1406 | stateGpu->copyCoordinatesFromGpu(state->x, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1442:55: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1442 | stateGpu->copyCoordinatesToGpu(state->x, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1450:58: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1450 | stateGpu->copyVelocitiesToGpu(state->v, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1468:21: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1468 | sum_dhdl(enerd, state->lambda, *ir->fepvals);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/replicaexchange.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In function 'void write_em_traj(FILE*, const t_commrec*, gmx_mdoutf_t, gmx_bool, gmx_bool, const char*, gmx_mtop_t*, t_inputrec*, int64_t, em_state_t*, t_state*, ObservablesHistory*)':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:533:37: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
533 | mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, top_global->natoms, step,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
534 | static_cast<double>(step), &state->s, state_global,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
535 | observablesHistory, state->f);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:545:31: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
545 | dd_collect_vec(cr->dd, &state->s, state->s.x, globalXRef);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In member function 'void {anonymous}::EnergyEvaluator::run(em_state_t*, real*, real (*)[3], real (*)[3], int64_t, gmx_bool)':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:845:13: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
845 | do_force(fplog, cr, ms, inputrec, nullptr, nullptr, imdSession, pull_work, count, nrnb, wcycle,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
846 | top, ems->s.box, ems->s.x.arrayRefWithPadding(), &ems->s.hist,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
847 | ems->f.arrayRefWithPadding(), force_vir, mdAtoms->mdatoms(), enerd, fcd, ems->s.lambda,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
848 | graph, fr, runScheduleWork, vsite, mu_tot, t, nullptr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
849 | GMX_FORCE_STATECHANGED | GMX_FORCE_ALLFORCES | GMX_FORCE_VIRIAL | GMX_FORCE_ENERGY
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
850 | | (bNS ? GMX_FORCE_NS : 0),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
851 | DDBalanceRegionHandler(cr));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:905:13: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
905 | sum_dhdl(enerd, ems->s.lambda, *inputrec->fepvals);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:54:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:54:
/usr/include/c++/9/bits/stl_vector.h: In function 'bool do_em_step(const t_commrec*, t_inputrec*, t_mdatoms*, em_state_t*, real, PaddedHostVector<gmx::BasicVector<double> >*, em_state_t*, gmx::Constraints*, int64_t)':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In function 'void init_em(FILE*, const gmx::MDLogger&, const char*, const t_commrec*, t_inputrec*, gmx::ImdSession*, pull_t*, t_state*, gmx_mtop_t*, em_state_t*, gmx_localtop_t*, t_nrnb*, t_forcerec*, t_graph**, gmx::MDAtoms*, gmx_global_stat**, gmx_vsite_t*, gmx::Constraints*, gmx_shellfc_t**)':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:385:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
385 | initialize_lambdas(fplog, *ir, MASTER(cr), &(state_global->fep_state), state_global->lambda, nullptr);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:54:
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In member function 'void gmx::LegacySimulator::do_lbfgs()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:1858:41: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1858 | mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, top_global->natoms, step,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1859 | static_cast<real>(step), &ems.s, state_global,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1860 | observablesHistory, ems.f);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/rerun.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In member function 'void gmx::LegacySimulator::do_nm()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:2766:40: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
2766 | relax_shell_flexcon(fplog, cr, ms, mdrunOptions.verbose, nullptr, step, inputrec,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2767 | imdSession, pull_work, bNS, force_flags, &top, constr, enerd,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2768 | fcd, state_work.s.natoms, state_work.s.x.arrayRefWithPadding(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2769 | state_work.s.v.arrayRefWithPadding(), state_work.s.box,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2770 | state_work.s.lambda, &state_work.s.hist,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2771 | state_work.f.arrayRefWithPadding(), vir, mdatoms, nrnb,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2772 | wcycle, graph, shellfc, fr, runScheduleWork, t, mu_tot,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2773 | vsite, DDBalanceRegionHandler(nullptr));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:52:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In member function 'void gmx::LegacySimulator::do_cg()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:533:37: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
533 | mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, top_global->natoms, step,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
534 | static_cast<double>(step), &state->s, state_global,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
535 | observablesHistory, state->f);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp: In member function 'void gmx::LegacySimulator::do_rerun()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:302:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
302 | initialize_lambdas(fplog, *ir, MASTER(cr), &state_global->fep_state, state_global->lambda, lam0);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:52:
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:551:32: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
551 | relax_shell_flexcon(fplog, cr, ms, mdrunOptions.verbose, enforcedRotation, step, ir,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
552 | imdSession, pull_work, bNS, force_flags, &top, constr, enerd, fcd,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
553 | state->natoms, state->x.arrayRefWithPadding(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
554 | state->v.arrayRefWithPadding(), state->box, state->lambda, &state->hist,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
555 | f.arrayRefWithPadding(), force_vir, mdatoms, nrnb, wcycle, graph,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
556 | shellfc, fr, runScheduleWork, t, mu_tot, vsite, ddBalanceRegionHandler);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:567:21: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
567 | do_force(fplog, cr, ms, ir, awh, enforcedRotation, imdSession, pull_work, step, nrnb,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
568 | wcycle, &top, state->box, state->x.arrayRefWithPadding(), &state->hist,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
569 | f.arrayRefWithPadding(), force_vir, mdatoms, enerd, fcd, state->lambda, graph,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
570 | fr, runScheduleWork, vsite, mu_tot, t, ed, GMX_FORCE_NS | force_flags,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
571 | ddBalanceRegionHandler);
| ~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:581:37: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
581 | do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t, ir, state,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
582 | state_global, observablesHistory, top_global, fr, outf,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
583 | energyOutput, ekind, f, isCheckpointingStep, doRerun,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
584 | isLastStep, mdrunOptions.writeConfout, bSumEkinhOld);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:641:21: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
641 | sum_dhdl(enerd, state->lambda, *ir->fepvals);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In member function 'void gmx::LegacySimulator::do_steep()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:533:37: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
533 | mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, top_global->natoms, step,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
534 | static_cast<double>(step), &state->s, state_global,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
535 | observablesHistory, state->f);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/shellfc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/simulationcontext.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/math/arrayrefwithpadding.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:40:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp: In function 'void relax_shell_flexcon(FILE*, const t_commrec*, const gmx_multisim_t*, gmx_bool, gmx_enfrot*, int64_t, const t_inputrec*, gmx::ImdSession*, pull_t*, gmx_bool, int, const gmx_localtop_t*, gmx::Constraints*, gmx_enerdata_t*, t_fcdata*, int, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, const real (*)[3], gmx::ArrayRef<double>, history_t*, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, real (*)[3], const t_mdatoms*, t_nrnb*, gmx_wallcycle_t, t_graph*, gmx_shellfc_t*, t_forcerec*, gmx::MdrunScheduleWorkload*, double, real*, const gmx_vsite_t*, const DDBalanceRegionHandler&)':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:936:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
936 | void relax_shell_flexcon(FILE* fplog,
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/math/arrayrefwithpadding.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:40:
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:1094:13: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
1094 | do_force(fplog, cr, ms, inputrec, nullptr, enforcedRotation, imdSession, pull_work, mdstep,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1095 | nrnb, wcycle, top, box, x, hist, forceWithPadding[Min], force_vir, md, enerd, fcd,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1096 | lambda, graph, fr, runScheduleWork, vsite, mu_tot, t, nullptr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1097 | (bDoNS ? GMX_FORCE_NS : 0) | shellfc_flags, ddBalanceRegionHandler);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:1188:17: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
1188 | do_force(fplog, cr, ms, inputrec, nullptr, enforcedRotation, imdSession, pull_work, 1, nrnb,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1189 | wcycle, top, box, posWithPadding[Try], hist, forceWithPadding[Try], force_vir, md,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1190 | enerd, fcd, lambda, graph, fr, runScheduleWork, vsite, mu_tot, t, nullptr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1191 | shellfc_flags, ddBalanceRegionHandler);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.cpp:46:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp:55:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/handlerestart.cpp
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.cpp:46:
/usr/include/c++/9/bits/stl_vector.h: In function 'void gmx::changePinningPolicy(PinnableVector*, gmx::PinningPolicy) [with PinnableVector = gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >]':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.cpp:46:
/usr/include/c++/9/bits/unique_ptr.h: In member function 'int gmx::Mdrunner::mdrunner()':
/usr/include/c++/9/bits/unique_ptr.h:857:30: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
857 | { return unique_ptr<_Tp>(new _Tp(std::forward<_Args>(__args)...)); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.cpp:1384:38: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1384 | constructVsitesGlobal(mtop, globalState->x);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp:55:
/usr/include/c++/9/bits/stl_vector.h: In member function 'void gmx::LegacySimulator::do_tpi()':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp:591:26: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
591 | nbnxn_put_on_grid(fr->nbv.get(), box, 0, vzero, boxDiagonal, nullptr, { 0, a_tp0 }, -1,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
592 | fr->cginfo, x, 0, nullptr);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp:663:34: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
663 | nbnxn_put_on_grid(fr->nbv.get(), box, 1, x_init, x_init, nullptr, { a_tp0, a_tp1 },
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
664 | -1, fr->cginfo, x, 0, nullptr);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp:722:40: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
722 | fr->nbv->convertCoordinates(AtomLocality::NonLocal, false, x);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp:722:40: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp:745:21: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
745 | do_force(fplog, cr, ms, inputrec, nullptr, nullptr, imdSession, pull_work, step, nrnb,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
746 | wcycle, &top, state_global->box, state_global->x.arrayRefWithPadding(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
747 | &state_global->hist, f.arrayRefWithPadding(), force_vir, mdatoms, enerd, fcd,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
748 | state_global->lambda, nullptr, fr, runScheduleWork, nullptr, mu_tot, t, nullptr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
749 | GMX_FORCE_NONBONDED | GMX_FORCE_ENERGY | (bStateChanged ? GMX_FORCE_STATECHANGED : 0),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
750 | DDBalanceRegionHandler(nullptr));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/logging.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/multisim.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/printtime.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/threadaffinity.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/abstractoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/abstractoption.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp: In member function 'void gmx::StatePropagatorDataGpu::copyCoordinatesToGpu(gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::AtomLocality)':
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp:132:6: note: parameter passing for argument of type 'const gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
132 | void StatePropagatorDataGpu::copyCoordinatesToGpu(const gmx::ArrayRef<const gmx::RVec> /* h_x */,
| ^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp: In member function 'void gmx::StatePropagatorDataGpu::copyCoordinatesFromGpu(gmx::ArrayRef<gmx::BasicVector<double> >, gmx::AtomLocality)':
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp:147:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
147 | void StatePropagatorDataGpu::copyCoordinatesFromGpu(gmx::ArrayRef<gmx::RVec> /* h_x */,
| ^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp: In member function 'void gmx::StatePropagatorDataGpu::copyVelocitiesToGpu(gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::AtomLocality)':
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp:164:6: note: parameter passing for argument of type 'const gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
164 | void StatePropagatorDataGpu::copyVelocitiesToGpu(const gmx::ArrayRef<const gmx::RVec> /* h_v */,
| ^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp: In member function 'void gmx::StatePropagatorDataGpu::copyVelocitiesFromGpu(gmx::ArrayRef<gmx::BasicVector<double> >, gmx::AtomLocality)':
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp:180:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
180 | void StatePropagatorDataGpu::copyVelocitiesFromGpu(gmx::ArrayRef<gmx::RVec> /* h_v */,
| ^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp: In member function 'void gmx::StatePropagatorDataGpu::copyForcesToGpu(gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::AtomLocality)':
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp:204:6: note: parameter passing for argument of type 'const gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
204 | void StatePropagatorDataGpu::copyForcesToGpu(const gmx::ArrayRef<const gmx::RVec> /* h_f */,
| ^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp: In member function 'void gmx::StatePropagatorDataGpu::copyForcesFromGpu(gmx::ArrayRef<gmx::BasicVector<double> >, gmx::AtomLocality)':
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp:229:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
229 | void StatePropagatorDataGpu::copyForcesFromGpu(gmx::ArrayRef<gmx::RVec> /* h_f */,
| ^~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/abstractsection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/abstractsection.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/basicoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/behaviorcollection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/behaviorcollection.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/filenameoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/filenameoption.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/filenameoptionmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/filenameoptionmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/options.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/options.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/optionsassigner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/optionsassigner.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/optionsection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/optionsection.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/optionsvisitor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/optionsvisitor.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/timeunitmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/timeunitmanager.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual void gmx::DoubleOptionStorage::processSetValues(gmx::OptionStorageTemplate<double>::ValueList*)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/treesupport.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/treesupport.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/restraint/manager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/restraint/manager.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/9/bits/stl_vector.h: In member function 'void gmx::OptionStorageTemplate<T>::addValue(const T&) [with T = double]':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreNull<T>::append(const T&) [with T = double]':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreVector<T>::append(const T&) [with T = double]':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<long long int, std::allocator<long long int> >::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/9/bits/stl_vector.h: In member function 'void gmx::OptionStorageTemplate<T>::addValue(const T&) [with T = long long int]':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreVector<T>::append(const T&) [with T = long long int]':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreNull<T>::append(const T&) [with T = long long int]':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/restraint/restraintmdmodule.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/restraint/restraintpotential.h:60,
from /<<PKGBUILDDIR>>/src/gromacs/restraint/restraintmdmodule.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/restraint/restraintmdmodule.cpp:38:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const int&}; _Tp = gmx::Site; _Alloc = std::allocator<gmx::Site>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::Site>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::Site*, std::vector<gmx::Site> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In constructor 'gmx::RestraintForceProvider::RestraintForceProvider(std::shared_ptr<gmx::IRestraintPotential>, const std::vector<int>&)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::Site*, std::vector<gmx::Site> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/decidegpuusage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/decidegpuusage.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/decidesimulationworkload.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/decidesimulationworkload.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/findallgputasks.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/findallgputasks.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/reportgpuusage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/reportgpuusage.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/resourcedivision.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/resourcedivision.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/taskassignment.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/taskassignment.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/usergpuids.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/usergpuids.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectory/energyframe.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectory/trajectoryframe.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mimic/communicator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mimic/utilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mimic/utilities.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o -c /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/baseversion-gen.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/checkpoint.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.h:39,
from /<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.cpp:37:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.cpp: In member function 'void gmx::MimicCommunicator::sendForces(gmx::ArrayRef<gmx::BasicVector<double> >, int)':
/<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.cpp:271:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
271 | void gmx::MimicCommunicator::sendForces(gmx::ArrayRef<gmx::RVec> forces, int natoms)
| ^~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.h:39,
from /<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.cpp:37:
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/confio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/confio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/enxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/enxio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/espio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/espio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/filetypes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/filetypes.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/g96io.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/gmx_internal_xdr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmx_internal_xdr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/gmxfio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/gmxfio_xdr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio_xdr.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.cpp:39:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {}; _Tp = gmx_file_position_t; _Alloc = std::allocator<gmx_file_position_t>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx_file_position_t>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx_file_position_t*, std::vector<gmx_file_position_t> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In function 'std::vector<gmx_file_position_t> gmx_fio_get_output_file_positions()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx_file_position_t*, std::vector<gmx_file_position_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/groio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/groio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/libxdrf.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/matio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/md5.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/md5.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/mrcdensitymap.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mrcdensitymap.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/mrcdensitymapheader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mrcdensitymapheader.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/mrcserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mrcserializer.cpp
/<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp: In function 'void writeXpmAxis(FILE*, const char*, gmx::ArrayRef<const double>)':
/<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp:809:13: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
809 | static void writeXpmAxis(FILE* out, const char* axis, ArrayRef<const real> label)
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp: In function 't_matelmt searchcmap(gmx::ArrayRef<const t_mapping>, t_xpmelmt)':
/<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp:114:11: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
114 | t_matelmt searchcmap(ArrayRef<const t_mapping> map, t_xpmelmt c)
| ^~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mtxio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/oenv.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/matio.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp:39:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/pdbio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/pdbio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/readinp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/readinp.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/timecontrol.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/timecontrol.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/tngio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tngio.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/tngio.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/tngio.cpp:37:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/tngio.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/tngio.cpp:37:
/usr/include/c++/9/bits/stl_vector.h: In function 'void gmx_tng_add_mtop(gmx_tng_trajectory_t, const gmx_mtop_t*)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tpxio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/trrio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/trrio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/trxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/trxio.cpp
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/matio.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp:39:
/usr/include/c++/9/bits/stl_vector.h: In function 'std::vector<t_matrix> read_xpm_matrix(const char*)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/vmdio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/vmdio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/warninp.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/writeps.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/writeps.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/writeps.cpp:39:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_rgb}; _Tp = t_rgb; _Alloc = std::allocator<t_rgb>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_rgb>::iterator' {aka '__gnu_cxx::__normal_iterator<t_rgb*, std::vector<t_rgb> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_rgb>::iterator' {aka '__gnu_cxx::__normal_iterator<t_rgb*, std::vector<t_rgb> >'} changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In function 'gmx::index search_col(t_psdata*, real, real, real)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_rgb*, std::vector<t_rgb> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/xdrd.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/xtcio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/xvgr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/centerofmass.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/centerofmass.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/compiler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/compiler.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/evaluate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/evaluate.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/indexutil.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/mempool.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/mempool.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/params.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/params.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/parsetree.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/poscalc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/poscalc.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/position.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/position.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/scanner_internal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/scanner_internal.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selection.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selectioncollection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selectioncollection.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selectionoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selectionoption.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/selection/selection.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/selection/selection.cpp:44:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/selection/selection.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/selection/selection.cpp:44:
/usr/include/c++/9/bits/stl_vector.h: In function 'void gmx::internal::{anonymous}::computeMassesAndCharges(const gmx_mtop_t*, const gmx_ana_pos_t&, std::vector<double>*, std::vector<double>*)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/selection/selection.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/selection/selection.cpp:44:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/selection/selection.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/selection/selection.cpp:44:
/usr/include/c++/9/bits/stl_vector.h: In member function 'void gmx::internal::SelectionData::initializeMassesAndCharges(const gmx_mtop_t*)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selectionoptionbehavior.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selectionoptionbehavior.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selectionoptionmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selectionoptionmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selelem.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selelem.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selhelp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selhelp.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selmethod.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selmethod.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selvalue.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selvalue.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/sm_compare.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_compare.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/sm_distance.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_distance.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/sm_insolidangle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_insolidangle.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/sm_keywords.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_keywords.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/sm_merge.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_merge.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/sm_permute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_permute.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/sm_position.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_position.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_same.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_simple.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/symrec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/symrec.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_system.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_system.cpp:46:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_system.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_system.cpp:46:
/usr/include/c++/9/bits/stl_vector.h: In constructor 'gmx::BenchmarkSystem::BenchmarkSystem(int)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cmake -E cmake_link_script CMakeFiles/libgromacs.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgromacs_d.so.5 -o ../../lib/libgromacs_d.so.5.0.0 CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o CMakeFiles/libgromacs.dir/utility/any.cpp.o CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o CMakeFiles/libgromacs.dir/utility/compare.cpp.o CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o 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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgromacs_d.so.5.0.0 ../../lib/libgromacs_d.so.5 ../../lib/libgromacs_d.so
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cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/share/template /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/share/template /<<PKGBUILDDIR>>/build/basic-dp/share/template/CMakeFiles/template.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs /<<PKGBUILDDIR>>/build/basic-dp/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/api/cpp /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/CMakeFiles/gmxapi.dir/DependInfo.cmake --color=
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make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/share/template && /usr/bin/c++ -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -std=c++14 -o CMakeFiles/template.dir/template.cpp.o -c /<<PKGBUILDDIR>>/share/template/template.cpp
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmx.dir/gmx.cpp.o -c /<<PKGBUILDDIR>>/src/programs/gmx.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmx.dir/legacymodules.cpp.o -c /<<PKGBUILDDIR>>/src/programs/legacymodules.cpp
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/context.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/context.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/exceptions.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/exceptions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/gmxapi.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/gmxapi.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/md.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/md.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmx.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gmx.dir/gmx.cpp.o CMakeFiles/gmx.dir/legacymodules.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o CMakeFiles/view_objlib.dir/view/3dview.cpp.o CMakeFiles/view_objlib.dir/view/buttons.cpp.o CMakeFiles/view_objlib.dir/view/dialogs.cpp.o CMakeFiles/view_objlib.dir/view/fgrid.cpp.o CMakeFiles/view_objlib.dir/view/filter.cpp.o CMakeFiles/view_objlib.dir/view/logo.cpp.o CMakeFiles/view_objlib.dir/view/manager.cpp.o CMakeFiles/view_objlib.dir/view/molps.cpp.o CMakeFiles/view_objlib.dir/view/nleg.cpp.o CMakeFiles/view_objlib.dir/view/nmol.cpp.o CMakeFiles/view_objlib.dir/view/popup.cpp.o CMakeFiles/view_objlib.dir/view/pulldown.cpp.o CMakeFiles/view_objlib.dir/view/view.cpp.o CMakeFiles/view_objlib.dir/view/x11.cpp.o CMakeFiles/view_objlib.dir/view/xdlg.cpp.o CMakeFiles/view_objlib.dir/view/xdlghi.cpp.o CMakeFiles/view_objlib.dir/view/xdlgitem.cpp.o CMakeFiles/view_objlib.dir/view/xmb.cpp.o CMakeFiles/view_objlib.dir/view/xutil.cpp.o -o ../../bin/gmx_d ../../lib/libgromacs_d.so.5.0.0 /usr/lib/arm-linux-gnueabihf/libX11.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 98%] Built target gmx
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/mdmodule.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/mdmodule.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/share/template && /usr/bin/cmake -E cmake_link_script CMakeFiles/template.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/template.dir/template.cpp.o -o ../../bin/template ../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 98%] Built target template
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/mdsignals.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/mdsignals.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/session.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/session.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/status.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/status.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/system.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/system.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/version.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/version.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/workflow.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/workflow.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/tpr.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tpr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgmxapi_d.so.0 -o ../../../lib/libgmxapi_d.so.0.1.0 CMakeFiles/gmxapi.dir/context.cpp.o CMakeFiles/gmxapi.dir/exceptions.cpp.o CMakeFiles/gmxapi.dir/gmxapi.cpp.o CMakeFiles/gmxapi.dir/md.cpp.o CMakeFiles/gmxapi.dir/mdmodule.cpp.o CMakeFiles/gmxapi.dir/mdsignals.cpp.o CMakeFiles/gmxapi.dir/session.cpp.o CMakeFiles/gmxapi.dir/status.cpp.o CMakeFiles/gmxapi.dir/system.cpp.o CMakeFiles/gmxapi.dir/version.cpp.o CMakeFiles/gmxapi.dir/workflow.cpp.o CMakeFiles/gmxapi.dir/tpr.cpp.o ../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libgmxapi_d.so.0.1.0 ../../../lib/libgmxapi_d.so.0 ../../../lib/libgmxapi_d.so
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cd /<<PKGBUILDDIR>> && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2020.3-Raspbian-2020.3-1 -D PROJECT_SOURCE_DIR=/<<PKGBUILDDIR>> -D DIRECTORIES_TO_CHECKSUM=src:python_packaging -D VERSION_CMAKEIN=/<<PKGBUILDDIR>>/build/basic/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/<<PKGBUILDDIR>>/build/basic/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Raspbian-2020.3-1 -P /<<PKGBUILDDIR>>/cmake/gmxGenerateVersionInfoRelease.cmake
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs /<<PKGBUILDDIR>>/build/basic/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/linearalgebra /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/linearalgebra /<<PKGBUILDDIR>>/build/basic/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/fileio /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/CMakeFiles/vmddlopen.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/external/googletest/googletest /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/external/googletest/googlemock/gtest /<<PKGBUILDDIR>>/build/basic/src/external/googletest/googlemock/gtest/CMakeFiles/gtest.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs /<<PKGBUILDDIR>>/build/basic/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic/src/external/googletest/googlemock/gtest && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_CREATE_SHARED_LIBRARY=1 -Dgtest_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/googletest/googletest/include -I/<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wshadow -DGTEST_HAS_PTHREAD=1 -fexceptions -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=c++14 -o CMakeFiles/gtest.dir/src/gtest-all.cc.o -c /<<PKGBUILDDIR>>/src/external/googletest/googletest/src/gtest-all.cc
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs /<<PKGBUILDDIR>>/build/basic/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color=
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[ 67%] Built target gmxapi
cd /<<PKGBUILDDIR>>/build/basic/src/external/googletest/googlemock/gtest && /usr/bin/cmake -E cmake_link_script CMakeFiles/gtest.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgtest.so -o ../../../../../lib/libgtest.so CMakeFiles/gtest.dir/src/gtest-all.cc.o -lpthread
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/usr/bin/make -f src/external/googletest/googlemock/CMakeFiles/gmock.dir/build.make src/external/googletest/googlemock/CMakeFiles/gmock.dir/depend
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/external/googletest/googlemock /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/external/googletest/googlemock /<<PKGBUILDDIR>>/build/basic/src/external/googletest/googlemock/CMakeFiles/gmock.dir/DependInfo.cmake --color=
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/external/googletest/googlemock && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_CAN_STREAM_RESULTS=0 -DGTEST_CREATE_SHARED_LIBRARY=1 -D_GNU_SOURCE=1 -Dgmock_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -I/<<PKGBUILDDIR>>/src/external/googletest/googlemock -I/<<PKGBUILDDIR>>/src/external/googletest/googletest -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wshadow -DGTEST_HAS_PTHREAD=1 -fexceptions -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -Wno-deprecated-copy -std=c++14 -o CMakeFiles/gmock.dir/src/gmock-all.cc.o -c /<<PKGBUILDDIR>>/src/external/googletest/googlemock/src/gmock-all.cc
cd /<<PKGBUILDDIR>>/build/basic/src/external/googletest/googlemock && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmock.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgmock.so -o ../../../../lib/libgmock.so CMakeFiles/gmock.dir/src/gmock-all.cc.o -lpthread ../../../../lib/libgtest.so -lpthread
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/usr/bin/make -f src/testutils/CMakeFiles/testutils.dir/build.make src/testutils/CMakeFiles/testutils.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/testutils /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/testutils /<<PKGBUILDDIR>>/build/basic/src/testutils/CMakeFiles/testutils.dir/DependInfo.cmake --color=
Scanning dependencies of target testutils
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cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/cmdlinetest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/cmdlinetest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/conftest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/conftest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/filematchers.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/filematchers.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/interactivetest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/interactivetest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/loggertest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/loggertest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/mpi_printer.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/mpi_printer.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/mpitest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/mpitest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/refdata.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/refdata.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/refdata_xml.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/refdata_xml.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/testutils/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/energycomparison.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -o ../../../bin/testutils-mpi-test ../../../lib/libtestutils.a ../../../lib/libgromacs.so.5.0.0 ../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/utility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
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[ 69%] Built target testutils-mpi-test
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/moduletest.cpp
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[ 70%] Built target utility-mpi-test
cd /<<PKGBUILDDIR>>/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-test.dir/refdata_tests.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tests/refdata_tests.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tests/testasserts_tests.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tests/xvgtest_tests.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/mdmodulenotification.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/mdmodulenotification.cpp
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/utility/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/CMakeFiles/utility-test.dir/DependInfo.cmake --color=
Scanning dependencies of target utility-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/alignedallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/alignedallocator.cpp
/usr/bin/make -f src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build.make src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdlib-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/calc_verletbuf.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/terminationhelper.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/constr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/trajectorycomparison.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/testutils-test.dir/interactivetest.cpp.o CMakeFiles/testutils-test.dir/refdata_tests.cpp.o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -o ../../../bin/testutils-test ../../../lib/libtestutils.a ../../../lib/libgromacs.so.5.0.0 ../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../lib/libgtest.so -lpthread
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[ 71%] Built target testutils-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/applied_forces/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/DependInfo.cmake --color=
Scanning dependencies of target applied_forces-test
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/densityfitting.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/tests/densityfitting.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/arrayref.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/arrayref.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/densityfittingoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/tests/densityfittingoptions.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/trajectoryreader.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/trajectoryreader.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -P CMakeFiles/mdrun_test_infrastructure.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun_test_infrastructure.dir/link.txt --verbose=1
/usr/bin/ar qc ../../../../lib/libmdrun_test_infrastructure.a CMakeFiles/mdrun_test_infrastructure.dir/energyreader.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/mdmodulenotification.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/trajectoryreader.cpp.o
/usr/bin/ranlib ../../../../lib/libmdrun_test_infrastructure.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 71%] Built target mdrun_test_infrastructure
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/densityfittingamplitudelookup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/tests/densityfittingamplitudelookup.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestdata.cpp
/usr/bin/make -f src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build.make src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/listed_forces/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/DependInfo.cmake --color=
Scanning dependencies of target listed_forces-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build.make src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/listed_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/listed_forces-test.dir/bonded.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestrunners.cpp
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:62,
from /<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:51:
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h: In function 'testing::internal::ParamGenerator<typename testing::internal::IteratorTraits<Iterator>::value_type> testing::ValuesIn(ForwardIterator, ForwardIterator) [with ForwardIterator = __gnu_cxx::__normal_iterator<const gmx::{anonymous}::iListInput*, std::vector<gmx::{anonymous}::iListInput> >]':
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h:310:1: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::{anonymous}::iListInput*, std::vector<gmx::{anonymous}::iListInput> >' changed in GCC 7.1
310 | ValuesIn(ForwardIterator begin, ForwardIterator end) {
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h:310:1: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::{anonymous}::iListInput*, std::vector<gmx::{anonymous}::iListInput> >' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:51:
/usr/include/c++/9/bits/stl_vector.h: In function 'std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = gmx::{anonymous}::iListInput; _Alloc = std::allocator<gmx::{anonymous}::iListInput>]':
/usr/include/c++/9/bits/stl_vector.h:622:7: note: parameter passing for argument of type 'std::initializer_list<gmx::{anonymous}::iListInput>' changed in GCC 7.1
622 | vector(initializer_list<value_type> __l,
| ^~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/ebin.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/ebin.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/electricfield.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/tests/electricfield.cpp
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:62,
from /<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:51:
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h: In function 'testing::internal::ParamGenerator<std::tuple<gmx::{anonymous}::iListInput, std::vector<gmx::BasicVector<float>, std::allocator<gmx::BasicVector<float> > >, int> > gmx::{anonymous}::gtest_RestraintsListedForcesTest_EvalGenerator_()':
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h:325:53: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::{anonymous}::iListInput*, std::vector<gmx::{anonymous}::iListInput> >' changed in GCC 7.1
325 | return ValuesIn(container.begin(), container.end());
| ^
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h: In function 'testing::internal::ParamGenerator<std::tuple<gmx::{anonymous}::iListInput, std::vector<gmx::BasicVector<float>, std::allocator<gmx::BasicVector<float> > >, int> > gmx::{anonymous}::gtest_PolarizeListedForcesTest_EvalGenerator_()':
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h:325:53: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::{anonymous}::iListInput*, std::vector<gmx::{anonymous}::iListInput> >' changed in GCC 7.1
325 | return ValuesIn(container.begin(), container.end());
| ^
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h: In function 'testing::internal::ParamGenerator<std::tuple<gmx::{anonymous}::iListInput, std::vector<gmx::BasicVector<float>, std::allocator<gmx::BasicVector<float> > >, int> > gmx::{anonymous}::gtest_DihedralListedForcesTest_EvalGenerator_()':
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h:325:53: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::{anonymous}::iListInput*, std::vector<gmx::{anonymous}::iListInput> >' changed in GCC 7.1
325 | return ValuesIn(container.begin(), container.end());
| ^
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h: In function 'testing::internal::ParamGenerator<std::tuple<gmx::{anonymous}::iListInput, std::vector<gmx::BasicVector<float>, std::allocator<gmx::BasicVector<float> > >, int> > gmx::{anonymous}::gtest_AngleListedForcesTest_EvalGenerator_()':
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h:325:53: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::{anonymous}::iListInput*, std::vector<gmx::{anonymous}::iListInput> >' changed in GCC 7.1
325 | return ValuesIn(container.begin(), container.end());
| ^
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h: In function 'testing::internal::ParamGenerator<std::tuple<gmx::{anonymous}::iListInput, std::vector<gmx::BasicVector<float>, std::allocator<gmx::BasicVector<float> > >, int> > gmx::{anonymous}::gtest_BondListedForcesTest_EvalGenerator_()':
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h:325:53: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::{anonymous}::iListInput*, std::vector<gmx::{anonymous}::iListInput> >' changed in GCC 7.1
325 | return ValuesIn(container.begin(), container.end());
| ^
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp: In function 'void __static_initialization_and_destruction_0(int, int)':
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:590:25: note: parameter passing for argument of type 'std::initializer_list<gmx::{anonymous}::iListInput>' changed in GCC 7.1
590 | std::vector<iListInput> c_InputBonds = {
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:605:25: note: parameter passing for argument of type 'std::initializer_list<gmx::{anonymous}::iListInput>' changed in GCC 7.1
605 | std::vector<iListInput> c_InputAngles = {
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:629:25: note: parameter passing for argument of type 'std::initializer_list<gmx::{anonymous}::iListInput>' changed in GCC 7.1
629 | std::vector<iListInput> c_InputDihs = {
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:639:25: note: parameter passing for argument of type 'std::initializer_list<gmx::{anonymous}::iListInput>' changed in GCC 7.1
639 | std::vector<iListInput> c_InputPols = {
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:647:25: note: parameter passing for argument of type 'std::initializer_list<gmx::{anonymous}::iListInput>' changed in GCC 7.1
647 | std::vector<iListInput> c_InputRestraints = {
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/energyoutput.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/energyoutput.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/listed_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/applied_forces-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/applied_forces-test.dir/densityfitting.cpp.o CMakeFiles/applied_forces-test.dir/densityfittingoptions.cpp.o CMakeFiles/applied_forces-test.dir/densityfittingamplitudelookup.cpp.o CMakeFiles/applied_forces-test.dir/electricfield.cpp.o CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/applied_forces-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/listed_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/listed_forces-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/listed_forces-test.dir/bonded.cpp.o CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/listed_forces-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
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/usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 72%] Built target listed_forces-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/bitmask32.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/bitmask32.cpp
Scanning dependencies of target onlinehelp-test-shared
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/mock_helptopic.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/cmake -P CMakeFiles/onlinehelp-test-shared.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test-shared.dir/link.txt --verbose=1
/usr/bin/ar qc ../../../../lib/libonlinehelp-test-shared.a CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o
/usr/bin/ranlib ../../../../lib/libonlinehelp-test-shared.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 72%] Built target onlinehelp-test-shared
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/bitmask64.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/bitmask64.cpp
/usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/domdec/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/DependInfo.cmake --color=
Scanning dependencies of target domdec-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/domdec-test.dir/hashedmap.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/tests/hashedmap.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/leapfrog.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrog.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/tests/localatomsetmanager.cpp
/usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/ewald/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/DependInfo.cmake --color=
Scanning dependencies of target ewald-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmebsplinetest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.cpp:43:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_grp_tcstat&}; _Tp = t_grp_tcstat; _Alloc = std::allocator<t_grp_tcstat>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_grp_tcstat>::iterator' {aka '__gnu_cxx::__normal_iterator<t_grp_tcstat*, std::vector<t_grp_tcstat> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/include/c++/9/bits/vector.tcc: In constructor 'gmx::test::LeapFrogTestData::LeapFrogTestData(int, real, const real*, const real*, int, int)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_grp_tcstat*, std::vector<t_grp_tcstat> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_grp_tcstat*, std::vector<t_grp_tcstat> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/domdec-test.dir/hashedmap.cpp.o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/domdec-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 72%] Built target domdec-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/bitmask128.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/bitmask128.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestrunners.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/settle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settle.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp
/usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/fft/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/fft/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/fft/tests/CMakeFiles/fft-test.dir/DependInfo.cmake --color=
Scanning dependencies of target fft-test
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fft/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fft/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fft-test.dir/fft.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/tests/fft.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/settletestdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settletestdata.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fft/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fft/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fft/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fft-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/fft-test.dir/fft.cpp.o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/fft-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/DependInfo.cmake --color=
Scanning dependencies of target gpu_utils-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/gputest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/gputest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settletestrunners.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/clfftinitializer.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesolvetest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/shake.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/shake.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/simulationsignal.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/cstringutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/cstringutil.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/defaultinitializationallocator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/updategroups.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroups.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/enumerationhelpers.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesplinespreadtest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/fixedcapacityvector.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroupscog.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/inmemoryserializer.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdlib-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o CMakeFiles/mdlib-test.dir/constr.cpp.o CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o CMakeFiles/mdlib-test.dir/ebin.cpp.o CMakeFiles/mdlib-test.dir/energyoutput.cpp.o CMakeFiles/mdlib-test.dir/leapfrog.cpp.o CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o CMakeFiles/mdlib-test.dir/settle.cpp.o CMakeFiles/mdlib-test.dir/settletestdata.cpp.o CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o CMakeFiles/mdlib-test.dir/shake.cpp.o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o CMakeFiles/mdlib-test.dir/updategroups.cpp.o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdlib-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 73%] Built target mdlib-test
/usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/hardware/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/hardware/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/DependInfo.cmake --color=
Scanning dependencies of target hardware-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/hardware/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/tests/hardwaretopology.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/keyvaluetreeserializer.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmetestcommon.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/hardware/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/hardware/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/hardware-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/hardware-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 73%] Built target hardware-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/devicetransfers.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/testhardwarecontexts.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/testhardwarecontexts.cpp
/usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/math/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/CMakeFiles/math-test.dir/DependInfo.cmake --color=
Scanning dependencies of target math-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/arrayrefwithpadding.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gpu_utils-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gpu_utils-test.dir/gputest.cpp.o CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gpu_utils-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 73%] Built target gpu_utils-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/coordinatetransformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/keyvaluetreetransform.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ewald-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o CMakeFiles/ewald-test.dir/testhardwarecontexts.cpp.o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/ewald-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 74%] Built target ewald-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/densityfit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/densityfit.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/math/arrayrefwithpadding.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/arrayrefwithpadding.cpp:43:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/math/arrayrefwithpadding.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/arrayrefwithpadding.cpp:43:
/usr/include/c++/9/bits/stl_vector.h: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::ArrayRefWithPaddingTest_AssignFromPaddedVectorWorks_Test<gmx::ArrayRefWithPadding<double> >]':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::ArrayRefWithPaddingTest_ConstructFromPointersWorks_Test<gmx::ArrayRefWithPadding<double> >]':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests/threadaffinitytest.cpp
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/DependInfo.cmake --color=
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests/accessor_policy.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/logger.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/logger.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/extents.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests/extents.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/dofit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/dofit.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/mutex.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/mutex.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/exponentialmovingaverage.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/extensions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests/extensions.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/cmake -P CMakeFiles/mdrunutility-test-shared.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test-shared.dir/link.txt --verbose=1
/usr/bin/ar qc ../../../../lib/libmdrunutility-test-shared.a CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/functions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/functions.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/layouts.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests/layouts.cpp
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/DependInfo.cmake --color=
Scanning dependencies of target onlinehelp-test
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/helpformat.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/functions.cpp:49:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvcbrtInteger_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/path.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/path.cpp
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_SixthrootDouble_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_SixthrootInteger_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_ErfInvDouble_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsixthrootInteger_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
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/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsixthrootDouble_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsqrtDouble_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsqrtInteger_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvcbrtDouble_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/mdspan.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests/mdspan.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/gausstransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/gausstransform.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/helpmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/physicalnodecommunicator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/stringutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/stringutil.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/helpwritercontext.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/densityfittingforce.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/densityfittingforce.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/onlinehelp-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 75%] Built target onlinehelp-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/invertmatrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/invertmatrix.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/textreader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/textreader.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/matrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/matrix.cpp
/usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/options/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/CMakeFiles/options-test.dir/DependInfo.cmake --color=
Scanning dependencies of target options-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/abstractoptionstorage.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/multidimarray.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/multidimarray.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdspan-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o CMakeFiles/mdspan-test.dir/extents.cpp.o CMakeFiles/mdspan-test.dir/extensions.cpp.o CMakeFiles/mdspan-test.dir/layouts.cpp.o CMakeFiles/mdspan-test.dir/mdspan.cpp.o CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdspan-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 75%] Built target mdspan-test
/usr/bin/make -f src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build.make src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/pbcutil/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/pbcutil/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/DependInfo.cmake --color=
Scanning dependencies of target pbcutil-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build.make src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/pbcutil/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pbcutil-test.dir/pbc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/tests/pbc.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/pbcutil/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/tests/pbcenums.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/paddedvector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/textwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/textwriter.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/pbcutil/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/typetraits.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/typetraits.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/pbcutil/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pbcutil-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pbcutil-test.dir/pbc.cpp.o CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pbcutil-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 75%] Built target pbcutil-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/filenameoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/filenameoption.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/utility-test.dir/alignedallocator.cpp.o CMakeFiles/utility-test.dir/arrayref.cpp.o CMakeFiles/utility-test.dir/bitmask32.cpp.o CMakeFiles/utility-test.dir/bitmask64.cpp.o CMakeFiles/utility-test.dir/bitmask128.cpp.o CMakeFiles/utility-test.dir/cstringutil.cpp.o CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o CMakeFiles/utility-test.dir/logger.cpp.o CMakeFiles/utility-test.dir/mutex.cpp.o CMakeFiles/utility-test.dir/path.cpp.o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o CMakeFiles/utility-test.dir/stringutil.cpp.o CMakeFiles/utility-test.dir/textreader.cpp.o CMakeFiles/utility-test.dir/textwriter.cpp.o CMakeFiles/utility-test.dir/typetraits.cpp.o CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/utility-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
/usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/random/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/CMakeFiles/random-test.dir/DependInfo.cmake --color=
Scanning dependencies of target random-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/exponentialdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/exponentialdistribution.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 76%] Built target utility-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/filenameoptionmanager.cpp
/usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/restraint/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/restraint/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/DependInfo.cmake --color=
Scanning dependencies of target restraintpotential-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/restraint/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/restraint/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/restraintpotential-test.dir/manager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/restraint/tests/manager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/gammadistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/gammadistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/restraint/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/restraint/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/restraint/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/restraintpotential-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/restraintpotential-test.dir/manager.cpp.o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/restraintpotential-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 76%] Built target restraintpotential-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/option.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/option.cpp
In file included from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:59:
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::fillInputContents(gmx::ArrayRef<gmx::BasicVector<ValueType> >, int) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:69:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
69 | void fillInputContents(ArrayRef<BasicVector<T>> inputRef, int scaleFactor)
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/optionsassigner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/optionsassigner.cpp
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::compareViews(gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:94:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
94 | void compareViews(ArrayRef<T> input, ArrayRef<T> output)
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:94:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::compareViews(gmx::ArrayRef<gmx::BasicVector<ValueType> >, gmx::ArrayRef<gmx::BasicVector<ValueType> >) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:105:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
105 | void compareViews(ArrayRef<BasicVector<T>> input, ArrayRef<BasicVector<T>> output)
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:105:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/tables/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/tables/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/tables/tests/CMakeFiles/table-test.dir/DependInfo.cmake --color=
Scanning dependencies of target table-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/tables/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/tables/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/table-test.dir/splinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/normaldistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/normaldistribution.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/9/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<double, std::allocator<double> >]':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<double, std::allocator<double> >]':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/9/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >]':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >]':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_NumericalInputPmeCorr_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::CubicSplineTable]':
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:515:15: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
515 | TypeParam pmeCorrTable({ { "NumericalPMECorr", functionValues, derivativeValues, inputSpacing } },
| ^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/seed.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/seed.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/9/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >]':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >]':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/9/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > >]':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > >]':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/tabulatednormaldistribution.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_NumericalInputPmeCorr_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::QuadraticSplineTable]':
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:515:15: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
515 | TypeParam pmeCorrTable({ { "NumericalPMECorr", functionValues, derivativeValues, inputSpacing } },
| ^~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_HandlesIncorrectNumericalInput_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::QuadraticSplineTable]':
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:457:13: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
457 | TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.001 } }, { 1.0, 2.0 }),
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:189:5: note: in expansion of macro 'GMX_TEST_THROW_'
189 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:456:5: note: in expansion of macro 'EXPECT_THROW_GMX'
456 | EXPECT_THROW_GMX(
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:463:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
463 | EXPECT_THROW_GMX(TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.1 } }, { 1.0, 2.0 }),
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:189:5: note: in expansion of macro 'GMX_TEST_THROW_'
189 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:463:5: note: in expansion of macro 'EXPECT_THROW_GMX'
463 | EXPECT_THROW_GMX(TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.1 } }, { 1.0, 2.0 }),
| ^~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:485:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
485 | EXPECT_THROW_GMX(TypeParam({ { "NumericalBadLJ12", functionValues, badDerivativeValues, spacing } },
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:189:5: note: in expansion of macro 'GMX_TEST_THROW_'
189 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:485:5: note: in expansion of macro 'EXPECT_THROW_GMX'
485 | EXPECT_THROW_GMX(TypeParam({ { "NumericalBadLJ12", functionValues, badDerivativeValues, spacing } },
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:492:13: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
492 | TypeParam({ { "NumericalLJ12", functionValues, derivativeValues, spacing } }, { 0.2, 1.0 }),
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:189:5: note: in expansion of macro 'GMX_TEST_THROW_'
189 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:491:5: note: in expansion of macro 'EXPECT_THROW_GMX'
491 | EXPECT_THROW_GMX(
| ^~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/vectypes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/vectypes.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/tabulatednormaldistribution.cpp:45:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_HandlesIncorrectNumericalInput_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::CubicSplineTable]':
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:457:13: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
457 | TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.001 } }, { 1.0, 2.0 }),
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:189:5: note: in expansion of macro 'GMX_TEST_THROW_'
189 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:456:5: note: in expansion of macro 'EXPECT_THROW_GMX'
456 | EXPECT_THROW_GMX(
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:463:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
463 | EXPECT_THROW_GMX(TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.1 } }, { 1.0, 2.0 }),
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:189:5: note: in expansion of macro 'GMX_TEST_THROW_'
189 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:463:5: note: in expansion of macro 'EXPECT_THROW_GMX'
463 | EXPECT_THROW_GMX(TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.1 } }, { 1.0, 2.0 }),
| ^~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:485:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
485 | EXPECT_THROW_GMX(TypeParam({ { "NumericalBadLJ12", functionValues, badDerivativeValues, spacing } },
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:189:5: note: in expansion of macro 'GMX_TEST_THROW_'
189 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:485:5: note: in expansion of macro 'EXPECT_THROW_GMX'
485 | EXPECT_THROW_GMX(TypeParam({ { "NumericalBadLJ12", functionValues, badDerivativeValues, spacing } },
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:492:13: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
492 | TypeParam({ { "NumericalLJ12", functionValues, derivativeValues, spacing } }, { 0.2, 1.0 }),
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:189:5: note: in expansion of macro 'GMX_TEST_THROW_'
189 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:491:5: note: in expansion of macro 'EXPECT_THROW_GMX'
491 | EXPECT_THROW_GMX(
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::TabulatedNormalDistributionTest_OutputDouble14_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/repeatingsection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/repeatingsection.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/threefry.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp
In file included from /usr/include/c++/9/vector:67,
from /usr/include/c++/9/bits/random.h:34,
from /usr/include/c++/9/random:49,
from /<<PKGBUILDDIR>>/src/gromacs/random/seed.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/random/threefry.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:43:
/usr/include/c++/9/bits/stl_vector.h: In constructor 'std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/9/bits/stl_vector.h:622:7: note: parameter passing for argument of type 'std::initializer_list<long long unsigned int>' changed in GCC 7.1
622 | vector(initializer_list<value_type> __l,
| ^~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/tables/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/tables/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/math-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o CMakeFiles/math-test.dir/coordinatetransformation.cpp.o CMakeFiles/math-test.dir/densityfit.cpp.o CMakeFiles/math-test.dir/dofit.cpp.o CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o CMakeFiles/math-test.dir/functions.cpp.o CMakeFiles/math-test.dir/gausstransform.cpp.o CMakeFiles/math-test.dir/densityfittingforce.cpp.o CMakeFiles/math-test.dir/invertmatrix.cpp.o CMakeFiles/math-test.dir/matrix.cpp.o CMakeFiles/math-test.dir/multidimarray.cpp.o CMakeFiles/math-test.dir/paddedvector.cpp.o CMakeFiles/math-test.dir/vectypes.cpp.o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/math-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp: In function 'void __static_initialization_and_destruction_0(int, int)':
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:117:54: note: parameter passing for argument of type 'std::initializer_list<long long unsigned int>' changed in GCC 7.1
117 | const std::vector<uint64_t> bitsZero{ { 0, 0, 0, 0 } };
| ^
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:127:87: note: parameter passing for argument of type 'std::initializer_list<long long unsigned int>' changed in GCC 7.1
127 | 0xFFFFFFFFFFFFFFFFULL, 0xFFFFFFFFFFFFFFFFULL } };
| ^
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:136:86: note: parameter passing for argument of type 'std::initializer_list<long long unsigned int>' changed in GCC 7.1
136 | 0xa4093822299f31d0ULL, 0x082efa98ec4e6c89ULL } };
| ^
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/tables/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/table-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/table-test.dir/splinetable.cpp.o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/table-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 77%] Built target math-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/timeunitmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/timeunitmanager.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 78%] Built target table-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/treesupport.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/treesupport.cpp
/usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/taskassignment/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/taskassignment/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/DependInfo.cmake --color=
Scanning dependencies of target taskassignment-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/taskassignment/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/taskassignment/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/tests/usergpuids.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/uniformintdistribution.cpp
/usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/topology/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests/CMakeFiles/topology-test.dir/DependInfo.cmake --color=
Scanning dependencies of target topology-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/topology-test.dir/exclusionblocks.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/tests/exclusionblocks.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/uniformrealdistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/topology-test.dir/mtop.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/tests/mtop.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/taskassignment/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/taskassignment/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/options-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o CMakeFiles/options-test.dir/filenameoption.cpp.o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o CMakeFiles/options-test.dir/option.cpp.o CMakeFiles/options-test.dir/optionsassigner.cpp.o CMakeFiles/options-test.dir/repeatingsection.cpp.o CMakeFiles/options-test.dir/timeunitmanager.cpp.o CMakeFiles/options-test.dir/treesupport.cpp.o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/options-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/topology-test.dir/symtab.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/tests/symtab.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 80%] Built target options-test
/usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/pulling/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/pulling/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/DependInfo.cmake --color=
Scanning dependencies of target pull-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/pulling/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/pulling/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pull-test.dir/pull.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/tests/pull.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/taskassignment/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/taskassignment-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/taskassignment-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 80%] Built target taskassignment-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/pulling/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/pulling/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/awh/tests/CMakeFiles/awh-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/awh/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/awh/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/awh/tests/CMakeFiles/awh-test.dir/DependInfo.cmake --color=
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/random-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/random-test.dir/exponentialdistribution.cpp.o CMakeFiles/random-test.dir/gammadistribution.cpp.o CMakeFiles/random-test.dir/normaldistribution.cpp.o CMakeFiles/random-test.dir/seed.cpp.o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o CMakeFiles/random-test.dir/threefry.cpp.o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/random-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
Scanning dependencies of target awh-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/awh-test.dir/bias.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/tests/bias.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 81%] Built target random-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/awh-test.dir/biasstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/tests/biasstate.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/pulling/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pull-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pull-test.dir/pull.cpp.o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pull-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 81%] Built target pull-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/awh-test.dir/grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/tests/grid.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/dimparams.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/awh/grid.h:60,
from /<<PKGBUILDDIR>>/src/gromacs/awh/tests/grid.cpp:37:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const float&, double, const float&}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void gmx::test::gridTest_neighborhood_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/awh/tests/biasstate.cpp:37:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double, double, double&}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In constructor 'gmx::test::BiasStateTest::BiasStateTest()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/topology-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/topology-test.dir/exclusionblocks.cpp.o CMakeFiles/topology-test.dir/mtop.cpp.o CMakeFiles/topology-test.dir/symtab.cpp.o CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/topology-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
/usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/simd/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/CMakeFiles/simd-test.dir/DependInfo.cmake --color=
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/bias.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/awh/tests/bias.cpp:37:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, double&, double&}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 81%] Built target topology-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/awh-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/include/c++/9/bits/vector.tcc: In function 'gmx::test::AwhTestParameters gmx::test::getAwhTestParameters(int, int)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
Scanning dependencies of target simd-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/bootstrap_loadstore.cpp
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/awh/bias.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/awh/tests/bias.cpp:37:
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual void gmx::test::BiasTest_ForcesBiasPmf_Test::TestBody()':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/bias.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/awh/tests/bias.cpp:37:
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/compat/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests/CMakeFiles/compat-test.dir/DependInfo.cmake --color=
Scanning dependencies of target compat-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -Wno-unused-member-function -o CMakeFiles/compat-test.dir/optional.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/compat/tests/optional.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/base.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/base.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/compat-test.dir/pointers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/compat/tests/pointers.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_floatingpoint.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_floatingpoint_util.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/compat-test.dir/string_view.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/compat/tests/string_view.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/awh/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/awh-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/awh-test.dir/bias.cpp.o CMakeFiles/awh-test.dir/biasstate.cpp.o CMakeFiles/awh-test.dir/grid.cpp.o CMakeFiles/awh-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/awh-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 81%] Built target awh-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_vector_operations.cpp
/usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/DependInfo.cmake --color=
Scanning dependencies of target gmxana-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxana-test.dir/entropy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/entropy.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_math.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_math.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/gmx_traj.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_memory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_memory.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_integer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_integer.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd4.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/gmx_mindist.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4_floatingpoint.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4_vector_operations.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxana-test.dir/gmx_msd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/gmx_msd.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd4_math.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4_math.cpp
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/DependInfo.cmake --color=
Scanning dependencies of target pdb2gmx3-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=1 -DCHARMM=1 -DGMX_DOUBLE=0 -DGROMOS=0 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/scalar.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/scalar.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxana-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gmxana-test.dir/entropy.cpp.o CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o CMakeFiles/gmxana-test.dir/gmx_msd.cpp.o CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gmxana-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 82%] Built target gmxana-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=1 -DCHARMM=1 -DGMX_DOUBLE=0 -DGROMOS=0 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/DependInfo.cmake --color=
Scanning dependencies of target pdb2gmx2-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=0 -DGROMOS=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/compat-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/compat-test.dir/optional.cpp.o CMakeFiles/compat-test.dir/pointers.cpp.o CMakeFiles/compat-test.dir/string_view.cpp.o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/compat-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/scalar_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/scalar_util.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 83%] Built target compat-test
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/DependInfo.cmake --color=
Scanning dependencies of target pdb2gmx1-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=0 -DGROMOS=0 -DHAVE_CONFIG_H -DOPLSAA=1 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx3-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pdb2gmx3-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 84%] Built target pdb2gmx3-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=0 -DGROMOS=0 -DHAVE_CONFIG_H -DOPLSAA=1 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/scalar_math.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/scalar_math.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=0 -DGROMOS=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/DependInfo.cmake --color=
Scanning dependencies of target gmxpreprocess-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/editconf.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx2-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pdb2gmx2-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 84%] Built target pdb2gmx2-test
/usr/bin/make -f src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build.make src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/DependInfo.cmake --color=
Scanning dependencies of target correlations-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/correlations-test.dir/autocorr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/autocorr.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx1-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pdb2gmx1-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/manyautocorrelation.cpp
[ 84%] Built target pdb2gmx1-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/correlations-test.dir/correlationdataset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/correlationdataset.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/simd-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o CMakeFiles/simd-test.dir/base.cpp.o CMakeFiles/simd-test.dir/simd.cpp.o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o CMakeFiles/simd-test.dir/simd_math.cpp.o CMakeFiles/simd-test.dir/simd_memory.cpp.o CMakeFiles/simd-test.dir/simd_integer.cpp.o CMakeFiles/simd-test.dir/simd4.cpp.o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o CMakeFiles/simd-test.dir/simd4_math.cpp.o CMakeFiles/simd-test.dir/scalar.cpp.o CMakeFiles/simd-test.dir/scalar_util.cpp.o CMakeFiles/simd-test.dir/scalar_math.cpp.o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/simd-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
/usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/DependInfo.cmake --color=
Scanning dependencies of target analysisdata-test-shared
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/datatest.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 85%] Built target simd-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/genconf.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/correlations-test.dir/expfit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/expfit.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/mock_datamodule.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/genion.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/genrestr.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/correlations-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/correlations-test.dir/autocorr.cpp.o CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o CMakeFiles/correlations-test.dir/correlationdataset.cpp.o CMakeFiles/correlations-test.dir/expfit.cpp.o CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/correlations-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
/usr/bin/make -f src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build.make src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 86%] Built target correlations-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_bond_atomtype.cpp
Scanning dependencies of target coordinateio-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/builder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/builder.cpp
/usr/bin/make -f src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build.make src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/energyanalysis/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/DependInfo.cmake --color=
Scanning dependencies of target energyanalysis-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/energyanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/legacyenergy.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/insert_molecules.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/energyanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/outputadaptercontainer.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/readir.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/energyanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/energyanalysis-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/energyanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 86%] Built target energyanalysis-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/solvate.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/outputadapters.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/requirements.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/requirements.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/topdirs.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/cmake -P CMakeFiles/analysisdata-test-shared.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test-shared.dir/link.txt --verbose=1
/usr/bin/ar qc ../../../../lib/libanalysisdata-test-shared.a CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o
/usr/bin/ranlib ../../../../lib/libanalysisdata-test-shared.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 86%] Built target analysisdata-test-shared
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/tools/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/CMakeFiles/tool-test.dir/DependInfo.cmake --color=
Scanning dependencies of target tool-test
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/usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/tool-test.dir/dump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/tests/dump.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxpreprocess-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gmxpreprocess-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 87%] Built target gmxpreprocess-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/tool-test.dir/report_methods.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/tests/report_methods.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/tool-test.dir/trjconv.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/tests/trjconv.cpp
/usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/fileio/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/DependInfo.cmake --color=
Scanning dependencies of target fileio-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/confio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/confio.cpp
/usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/selection/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests/CMakeFiles/selection-test.dir/DependInfo.cmake --color=
Scanning dependencies of target selection-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/indexutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/indexutil.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/filemd5.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/filemd5.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/tool-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/tool-test.dir/dump.cpp.o CMakeFiles/tool-test.dir/report_methods.cpp.o CMakeFiles/tool-test.dir/trjconv.cpp.o CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/tool-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 88%] Built target tool-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/mrcserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcserializer.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymap.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/nbsearch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/setatoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/setatoms.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymapheader.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/setbothtime.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/poscalc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/poscalc.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/setstarttime.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/readinp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/readinp.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/settimestep.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/settimestep.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/testmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/testmodule.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/fileioxdrserializer.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/tngio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/tngio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/selectioncollection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/selectioncollection.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/coordinateio-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/coordinateio-test.dir/builder.cpp.o CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o CMakeFiles/coordinateio-test.dir/requirements.cpp.o CMakeFiles/coordinateio-test.dir/setatoms.cpp.o CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o CMakeFiles/coordinateio-test.dir/settimestep.cpp.o CMakeFiles/coordinateio-test.dir/testmodule.cpp.o CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/coordinateio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-mpi-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/domain_decomposition.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 88%] Built target coordinateio-test
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/minimize.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/minimize.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileio-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/fileio-test.dir/confio.cpp.o CMakeFiles/fileio-test.dir/filemd5.cpp.o CMakeFiles/fileio-test.dir/mrcserializer.cpp.o CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o CMakeFiles/fileio-test.dir/readinp.cpp.o CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o CMakeFiles/fileio-test.dir/tngio.cpp.o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/fileio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 89%] Built target fileio-test
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/mimic.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/selectionoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/selectionoption.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/toputils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/toputils.cpp
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/compressed_x_output.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/compressed_x_output.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/multisim.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/multisim.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/densityfittingmodule.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/densityfittingmodule.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/exactcontinuation.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/exactcontinuation.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/multisimtest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/multisimtest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/pmetest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/pmetest.cpp
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-non-integrator-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-non-integrator-test.dir/minimize.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/minimize.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/replicaexchange.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/replicaexchange.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/selection-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/selection-test.dir/indexutil.cpp.o CMakeFiles/selection-test.dir/nbsearch.cpp.o CMakeFiles/selection-test.dir/poscalc.cpp.o CMakeFiles/selection-test.dir/selectioncollection.cpp.o CMakeFiles/selection-test.dir/selectionoption.cpp.o CMakeFiles/selection-test.dir/toputils.cpp.o CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/selection-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 90%] Built target selection-test
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-tpi-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/tpitest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/grompp.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/grompp.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/helpwriting.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/helpwriting.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o CMakeFiles/mdrun-mpi-test.dir/minimize.cpp.o CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o CMakeFiles/mdrun-mpi-test.dir/multisim.cpp.o CMakeFiles/mdrun-mpi-test.dir/multisimtest.cpp.o CMakeFiles/mdrun-mpi-test.dir/pmetest.cpp.o CMakeFiles/mdrun-mpi-test.dir/replicaexchange.cpp.o CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 90%] Built target mdrun-mpi-test
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-mpi-coordination-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-coordination-test.dir/periodicactions.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/periodicactions.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/initialconstraints.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/initialconstraints.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-tpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-tpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 91%] Built target mdrun-tpi-test
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/interactiveMD.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/interactiveMD.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/nonbonded_bench.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/normalmodes.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/outputfiles.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/outputfiles.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-coordination-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/rerun.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/simple_mdrun.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-coordination-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-mpi-coordination-test.dir/periodicactions.cpp.o CMakeFiles/mdrun-mpi-coordination-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-coordination-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 92%] Built target mdrun-mpi-coordination-test
/usr/bin/make -f src/api/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/build.make src/api/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/api/cpp/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/DependInfo.cmake --color=
Scanning dependencies of target gmxapi-mpi-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/restraint.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/restraint.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/orires.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/orires.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/status.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/status.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/pmetest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/pmetest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/system.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/system.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/version.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/version.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-non-integrator-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-non-integrator-test.dir/minimize.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-non-integrator-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
/usr/bin/make -f src/api/cpp/tests/CMakeFiles/gmxapi-test.dir/build.make src/api/cpp/tests/CMakeFiles/gmxapi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/api/cpp/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/CMakeFiles/gmxapi-test.dir/DependInfo.cmake --color=
Scanning dependencies of target gmxapi-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/restraint.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/restraint.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 93%] Built target mdrun-non-integrator-test
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/api/cpp/workflow/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests /<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests/CMakeFiles/workflow-details-mpi-test.dir/DependInfo.cmake --color=
Scanning dependencies of target workflow-details-mpi-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/api/cpp/workflow/tests/CMakeFiles/workflow-details-mpi-test.dir/build.make src/api/cpp/workflow/tests/CMakeFiles/workflow-details-mpi-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/workflow-details-mpi-test.dir/workflow.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/workflow/tests/workflow.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/simulator.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/simulator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/runner.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/runner.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/status.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/status.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/workflow-details-mpi-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/system.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/system.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/workflow-details-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/workflow-details-mpi-test.dir/workflow.cpp.o CMakeFiles/workflow-details-mpi-test.dir/__/__/__/__/testutils/unittest_main.cpp.o ../../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../../bin/workflow-details-mpi-test ../../../../../lib/libtestutils.a ../../../../../lib/libgmxapi.so.0.1.0 ../../../../../lib/libmdrun_test_infrastructure.a ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../../lib/libgmock.so ../../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/stopsignaler.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/stopsignaler.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 93%] Built target workflow-details-mpi-test
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/version.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/version.cpp
/usr/bin/make -f src/api/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build.make src/api/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/api/cpp/workflow/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests /<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/DependInfo.cmake --color=
Scanning dependencies of target workflow-details-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/api/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build.make src/api/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/workflow-details-test.dir/workflow.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/workflow/tests/workflow.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/runner.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/runner.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gmxapi-mpi-test.dir/restraint.cpp.o CMakeFiles/gmxapi-mpi-test.dir/status.cpp.o CMakeFiles/gmxapi-mpi-test.dir/system.cpp.o CMakeFiles/gmxapi-mpi-test.dir/version.cpp.o CMakeFiles/gmxapi-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/gmxapi-mpi-test.dir/runner.cpp.o CMakeFiles/gmxapi-mpi-test.dir/stopsignaler.cpp.o ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/gmxapi-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgmxapi.so.0.1.0 ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/workflow-details-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/swapcoords.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/swapcoords.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 93%] Built target gmxapi-mpi-test
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/stopsignaler.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/workflow-details-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/workflow-details-test.dir/workflow.cpp.o CMakeFiles/workflow-details-test.dir/__/__/__/__/testutils/unittest_main.cpp.o ../../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../../bin/workflow-details-test ../../../../../lib/libtestutils.a ../../../../../lib/libgmxapi.so.0.1.0 ../../../../../lib/libmdrun_test_infrastructure.a ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../../lib/libgmock.so ../../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 94%] Built target workflow-details-test
/usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/commandline/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/DependInfo.cmake --color=
Scanning dependencies of target commandline-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinehelpmodule.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/tabulated_bonded_interactions.cpp
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrunutility-mpi-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests/threadaffinity_mpi.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/termination.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/termination.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gmxapi-test.dir/restraint.cpp.o CMakeFiles/gmxapi-test.dir/status.cpp.o CMakeFiles/gmxapi-test.dir/system.cpp.o CMakeFiles/gmxapi-test.dir/version.cpp.o CMakeFiles/gmxapi-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/gmxapi-test.dir/runner.cpp.o CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/gmxapi-test ../../../../lib/libtestutils.a ../../../../lib/libgmxapi.so.0.1.0 ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 95%] Built target gmxapi-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinehelpwriter.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrunutility-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests/threadaffinity.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinemodulemanager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdrunutility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 96%] Built target mdrunutility-mpi-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/trajectory_writing.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/trajectory_writing.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/mimic.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/mimic.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdrunutility-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 96%] Built target mdrunutility-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinemodulemanagertest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlineparser.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-test.dir/compressed_x_output.cpp.o CMakeFiles/mdrun-test.dir/densityfittingmodule.cpp.o CMakeFiles/mdrun-test.dir/exactcontinuation.cpp.o CMakeFiles/mdrun-test.dir/grompp.cpp.o CMakeFiles/mdrun-test.dir/helpwriting.cpp.o CMakeFiles/mdrun-test.dir/initialconstraints.cpp.o CMakeFiles/mdrun-test.dir/interactiveMD.cpp.o CMakeFiles/mdrun-test.dir/outputfiles.cpp.o CMakeFiles/mdrun-test.dir/orires.cpp.o CMakeFiles/mdrun-test.dir/pmetest.cpp.o CMakeFiles/mdrun-test.dir/simulator.cpp.o CMakeFiles/mdrun-test.dir/swapcoords.cpp.o CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o CMakeFiles/mdrun-test.dir/termination.cpp.o CMakeFiles/mdrun-test.dir/trajectory_writing.cpp.o CMakeFiles/mdrun-test.dir/mimic.cpp.o CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 97%] Built target mdrun-test
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/analysisdata.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlineprogramcontext.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/filenm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/filenm.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/pargs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/pargs.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/analysisdata-test.dir/arraydata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/arraydata.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/analysisdata-test.dir/average.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/average.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/commandline-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o CMakeFiles/commandline-test.dir/filenm.cpp.o CMakeFiles/commandline-test.dir/pargs.cpp.o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/commandline-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/analysisdata-test.dir/histogram.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/histogram.cpp
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/DependInfo.cmake --color=
Scanning dependencies of target trajectoryanalysis-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/moduletest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/analysisdata-test.dir/lifetime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/lifetime.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/cmdlinerunner.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/angle.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/convert_trj.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/distance.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/extract_cluster.cpp
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/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o CMakeFiles/analysisdata-test.dir/arraydata.cpp.o CMakeFiles/analysisdata-test.dir/average.cpp.o CMakeFiles/analysisdata-test.dir/histogram.cpp.o CMakeFiles/analysisdata-test.dir/lifetime.cpp.o CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/analysisdata-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 98%] Built target analysisdata-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/pairdist.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/rdf.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/sasa.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/select.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/topologyinformation.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/trajectory.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/unionfind.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/trajectoryanalysis-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/trajectoryanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[100%] Built target trajectoryanalysis-test
/usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/CMakeFiles/tests.dir/DependInfo.cmake --color=
Scanning dependencies of target tests
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
make[4]: Nothing to be done for 'CMakeFiles/tests.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[100%] Built target tests
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/build/basic/CMakeFiles 0
make[2]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
make[1]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
(cd build/basic; LD_LIBRARY_PATH=/<<PKGBUILDDIR>>/build/basic/lib ctest -V || dpkg-architecture -i hurd-i386 )
UpdateCTestConfiguration from :/<<PKGBUILDDIR>>/build/basic/DartConfiguration.tcl
Parse Config file:/<<PKGBUILDDIR>>/build/basic/DartConfiguration.tcl
UpdateCTestConfiguration from :/<<PKGBUILDDIR>>/build/basic/DartConfiguration.tcl
Parse Config file:/<<PKGBUILDDIR>>/build/basic/DartConfiguration.tcl
Test project /<<PKGBUILDDIR>>/build/basic
Constructing a list of tests
Done constructing a list of tests
Updating test list for fixtures
Added 0 tests to meet fixture requirements
Checking test dependency graph...
Checking test dependency graph end
test 1
Start 1: TestUtilsUnitTests
1: Test command: /<<PKGBUILDDIR>>/build/basic/bin/testutils-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/TestUtilsUnitTests.xml"
1: Test timeout computed to be: 30
1: [==========] Running 59 tests from 5 test cases.
1: [----------] Global test environment set-up.
1: [----------] 10 tests from InteractiveTestHelperTest
1: [ RUN ] InteractiveTestHelperTest.ChecksSimpleSession
1: [ OK ] InteractiveTestHelperTest.ChecksSimpleSession (4 ms)
1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline
1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline (2 ms)
1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput
1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput (1 ms)
1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput
1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput (2 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsIncorrectOutput
1: [ OK ] InteractiveTestHelperTest.DetectsIncorrectOutput (2 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsMissingOutput
1: [ OK ] InteractiveTestHelperTest.DetectsMissingOutput (2 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsMissingFinalOutput
1: [ OK ] InteractiveTestHelperTest.DetectsMissingFinalOutput (2 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsExtraOutput
1: [ OK ] InteractiveTestHelperTest.DetectsExtraOutput (2 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsMissingInput
1: [ OK ] InteractiveTestHelperTest.DetectsMissingInput (1 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsExtraInput
1: [ OK ] InteractiveTestHelperTest.DetectsExtraInput (2 ms)
1: [----------] 10 tests from InteractiveTestHelperTest (20 ms total)
1:
1: [----------] 34 tests from ReferenceDataTest
1: [ RUN ] ReferenceDataTest.HandlesSimpleData
1: [ OK ] ReferenceDataTest.HandlesSimpleData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesFloatingPointData
1: [ OK ] ReferenceDataTest.HandlesFloatingPointData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesPresenceChecks
1: [ OK ] ReferenceDataTest.HandlesPresenceChecks (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesStringBlockData
1: [ OK ] ReferenceDataTest.HandlesStringBlockData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesVectorData
1: [ OK ] ReferenceDataTest.HandlesVectorData (2 ms)
1: [ RUN ] ReferenceDataTest.HandlesSequenceData
1: [ OK ] ReferenceDataTest.HandlesSequenceData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesSequenceOfCustomData
1: [ OK ] ReferenceDataTest.HandlesSequenceOfCustomData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesIncorrectData
1: [ OK ] ReferenceDataTest.HandlesIncorrectData (3 ms)
1: [ RUN ] ReferenceDataTest.HandlesIncorrectDataType
1: [ OK ] ReferenceDataTest.HandlesIncorrectDataType (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesMissingData
1: [ OK ] ReferenceDataTest.HandlesMissingData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesUncheckedData
1: [ OK ] ReferenceDataTest.HandlesUncheckedData (2 ms)
1: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInSequence
1: [ OK ] ReferenceDataTest.HandlesUncheckedDataInSequence (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInCompound
1: [ OK ] ReferenceDataTest.HandlesUncheckedDataInCompound (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesAnys
1: [ OK ] ReferenceDataTest.HandlesAnys (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesKeyValueTree
1: [ OK ] ReferenceDataTest.HandlesKeyValueTree (3 ms)
1: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeExtraKey
1: [ OK ] ReferenceDataTest.HandlesKeyValueTreeExtraKey (3 ms)
1: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeMissingKey
1: [ OK ] ReferenceDataTest.HandlesKeyValueTreeMissingKey (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectValue
1: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectValue (2 ms)
1: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectType
1: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectType (2 ms)
1: [ RUN ] ReferenceDataTest.HandlesMissingReferenceDataFile
1: [ OK ] ReferenceDataTest.HandlesMissingReferenceDataFile (0 ms)
1: [ RUN ] ReferenceDataTest.HandlesSpecialCharactersInStrings
1: [ OK ] ReferenceDataTest.HandlesSpecialCharactersInStrings (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace
1: [ OK ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesEmptyStrings
1: [ OK ] ReferenceDataTest.HandlesEmptyStrings (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock
1: [ OK ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock (0 ms)
1: [ RUN ] ReferenceDataTest.HandlesSequenceItemIndices
1: [ OK ] ReferenceDataTest.HandlesSequenceItemIndices (2 ms)
1: [ RUN ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData
1: [ OK ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesMultipleNullIds
1: [ OK ] ReferenceDataTest.HandlesMultipleNullIds (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds
1: [ OK ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds (2 ms)
1: [ RUN ] ReferenceDataTest.HandlesReadingValues
1: [ OK ] ReferenceDataTest.HandlesReadingValues (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges
1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges
1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges (2 ms)
1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges
1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges
1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges (2 ms)
1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries
1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries (1 ms)
1: [----------] 34 tests from ReferenceDataTest (50 ms total)
1:
1: [----------] 7 tests from FloatingPointDifferenceTest
1: [ RUN ] FloatingPointDifferenceTest.HandlesEqualValues
1: [ OK ] FloatingPointDifferenceTest.HandlesEqualValues (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesFloatValues
1: [ OK ] FloatingPointDifferenceTest.HandlesFloatValues (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign
1: [ OK ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero
1: [ OK ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferences
1: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferences (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero
1: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesNaN
1: [ OK ] FloatingPointDifferenceTest.HandlesNaN (0 ms)
1: [----------] 7 tests from FloatingPointDifferenceTest (0 ms total)
1:
1: [----------] 4 tests from FloatingPointToleranceTest
1: [ RUN ] FloatingPointToleranceTest.UlpTolerance
1: [ OK ] FloatingPointToleranceTest.UlpTolerance (0 ms)
1: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint
1: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint (0 ms)
1: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsUlp
1: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsUlp (0 ms)
1: [ RUN ] FloatingPointToleranceTest.DefaultFloatTolerance
1: [ OK ] FloatingPointToleranceTest.DefaultFloatTolerance (0 ms)
1: [----------] 4 tests from FloatingPointToleranceTest (0 ms total)
1:
1: [----------] 4 tests from XvgTests
1: [ RUN ] XvgTests.CreateFile
1: [ OK ] XvgTests.CreateFile (2 ms)
1: [ RUN ] XvgTests.CheckMissing
1: [ OK ] XvgTests.CheckMissing (1 ms)
1: [ RUN ] XvgTests.CheckExtra
1: [ OK ] XvgTests.CheckExtra (2 ms)
1: [ RUN ] XvgTests.ReadIncorrect
1: [ OK ] XvgTests.ReadIncorrect (2 ms)
1: [----------] 4 tests from XvgTests (9 ms total)
1:
1: [----------] Global test environment tear-down
1: [==========] 59 tests from 5 test cases ran. (80 ms total)
1: [ PASSED ] 59 tests.
1/52 Test #1: TestUtilsUnitTests .................. Passed 0.96 sec
test 2
Start 2: TestUtilsMpiUnitTests
2: Test command: /<<PKGBUILDDIR>>/build/basic/bin/testutils-mpi-test "-ntmpi" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/TestUtilsMpiUnitTests.xml"
2: Test timeout computed to be: 30
2: [==========] Running 1 test from 1 test case.
2: [----------] Global test environment set-up.
2: [----------] 1 test from MpiSelfTest
2: [ RUN ] MpiSelfTest.Runs
2: [ OK ] MpiSelfTest.Runs (20 ms)
2: [----------] 1 test from MpiSelfTest (20 ms total)
2:
2: [----------] Global test environment tear-down
2: [==========] 1 test from 1 test case ran. (20 ms total)
2: [ PASSED ] 1 test.
2/52 Test #2: TestUtilsMpiUnitTests ............... Passed 0.08 sec
test 3
Start 3: UtilityUnitTests
3: Test command: /<<PKGBUILDDIR>>/build/basic/bin/utility-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/UtilityUnitTests.xml"
3: Test timeout computed to be: 30
3: [==========] Running 347 tests from 56 test cases.
3: [----------] Global test environment set-up.
3: [----------] 5 tests from AllocatorTest/0, where TypeParam = gmx::Allocator<float, gmx::AlignedAllocationPolicy>
3: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment
3: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment
3: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment
3: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/0.Move
3: [ OK ] AllocatorTest/0.Move (0 ms)
3: [ RUN ] AllocatorTest/0.StatelessAllocatorUsesNoMemory
3: [ OK ] AllocatorTest/0.StatelessAllocatorUsesNoMemory (0 ms)
3: [----------] 5 tests from AllocatorTest/0 (1 ms total)
3:
3: [----------] 5 tests from AllocatorTest/1, where TypeParam = gmx::Allocator<float, gmx::PageAlignedAllocationPolicy>
3: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment
3: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment
3: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment
3: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/1.Move
3: [ OK ] AllocatorTest/1.Move (0 ms)
3: [ RUN ] AllocatorTest/1.StatelessAllocatorUsesNoMemory
3: [ OK ] AllocatorTest/1.StatelessAllocatorUsesNoMemory (0 ms)
3: [----------] 5 tests from AllocatorTest/1 (1 ms total)
3:
3: [----------] 5 tests from AllocatorTest/2, where TypeParam = gmx::Allocator<int, gmx::AlignedAllocationPolicy>
3: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment
3: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment
3: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment
3: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/2.Move
3: [ OK ] AllocatorTest/2.Move (0 ms)
3: [ RUN ] AllocatorTest/2.StatelessAllocatorUsesNoMemory
3: [ OK ] AllocatorTest/2.StatelessAllocatorUsesNoMemory (0 ms)
3: [----------] 5 tests from AllocatorTest/2 (1 ms total)
3:
3: [----------] 5 tests from AllocatorTest/3, where TypeParam = gmx::Allocator<int, gmx::PageAlignedAllocationPolicy>
3: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment
3: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment
3: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (1 ms)
3: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment
3: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/3.Move
3: [ OK ] AllocatorTest/3.Move (0 ms)
3: [ RUN ] AllocatorTest/3.StatelessAllocatorUsesNoMemory
3: [ OK ] AllocatorTest/3.StatelessAllocatorUsesNoMemory (0 ms)
3: [----------] 5 tests from AllocatorTest/3 (1 ms total)
3:
3: [----------] 5 tests from AllocatorTest/4, where TypeParam = gmx::Allocator<gmx::BasicVector<float>, gmx::AlignedAllocationPolicy>
3: [ RUN ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment
3: [ OK ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment
3: [ OK ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment (1 ms)
3: [ RUN ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment
3: [ OK ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/4.Move
3: [ OK ] AllocatorTest/4.Move (0 ms)
3: [ RUN ] AllocatorTest/4.StatelessAllocatorUsesNoMemory
3: [ OK ] AllocatorTest/4.StatelessAllocatorUsesNoMemory (0 ms)
3: [----------] 5 tests from AllocatorTest/4 (1 ms total)
3:
3: [----------] 5 tests from AllocatorTest/5, where TypeParam = gmx::Allocator<gmx::BasicVector<float>, gmx::PageAlignedAllocationPolicy>
3: [ RUN ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment
3: [ OK ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment
3: [ OK ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment (1 ms)
3: [ RUN ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment
3: [ OK ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/5.Move
3: [ OK ] AllocatorTest/5.Move (0 ms)
3: [ RUN ] AllocatorTest/5.StatelessAllocatorUsesNoMemory
3: [ OK ] AllocatorTest/5.StatelessAllocatorUsesNoMemory (0 ms)
3: [----------] 5 tests from AllocatorTest/5 (2 ms total)
3:
3: [----------] 1 test from AllocatorUntypedTest
3: [ RUN ] AllocatorUntypedTest.Comparison
3: [ OK ] AllocatorUntypedTest.Comparison (0 ms)
3: [----------] 1 test from AllocatorUntypedTest (0 ms total)
3:
3: [----------] 1 test from EmptyArrayRefTest
3: [ RUN ] EmptyArrayRefTest.IsEmpty
3: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms)
3: [----------] 1 test from EmptyArrayRefTest (0 ms total)
3:
3: [----------] 1 test from EmptyConstArrayRefTest
3: [ RUN ] EmptyConstArrayRefTest.IsEmpty
3: [ OK ] EmptyConstArrayRefTest.IsEmpty (0 ms)
3: [----------] 1 test from EmptyConstArrayRefTest (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef<char>
3: [ RUN ] ArrayRefTest/0.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/0.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/0.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/0.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/0.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/0.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/0.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/0.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/0 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef<unsigned char>
3: [ RUN ] ArrayRefTest/1.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/1.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/1.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/1.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/1.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/1.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/1.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/1.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/1 (1 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef<int>
3: [ RUN ] ArrayRefTest/2.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/2.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/2.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/2.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/2.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/2.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/2.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/2.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/2 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef<unsigned int>
3: [ RUN ] ArrayRefTest/3.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/3.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/3.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/3.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/3.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/3.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/3.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/3.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/3 (1 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/4, where TypeParam = gmx::ArrayRef<long>
3: [ RUN ] ArrayRefTest/4.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/4.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/4.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/4.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/4.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/4.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/4.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/4.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/4.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/4.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/4 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/5, where TypeParam = gmx::ArrayRef<unsigned long>
3: [ RUN ] ArrayRefTest/5.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/5.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/5.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/5.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/5.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/5.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/5.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/5.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/5.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/5.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/5 (1 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/6, where TypeParam = gmx::ArrayRef<long long>
3: [ RUN ] ArrayRefTest/6.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/6.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/6.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/6.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/6.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/6.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/6.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/6.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/6.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/6.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/6 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/7, where TypeParam = gmx::ArrayRef<unsigned long long>
3: [ RUN ] ArrayRefTest/7.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/7.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/7.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/7.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/7.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/7.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/7.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/7.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/7.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/7.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/7 (1 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/8, where TypeParam = gmx::ArrayRef<float>
3: [ RUN ] ArrayRefTest/8.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/8.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/8.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/8.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/8.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/8.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/8.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/8.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/8.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/8.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/8 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/9, where TypeParam = gmx::ArrayRef<double>
3: [ RUN ] ArrayRefTest/9.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/9.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/9.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/9.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/9.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/9.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/9.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/9.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/9.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/9.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/9 (1 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/10, where TypeParam = gmx::ArrayRef<char const>
3: [ RUN ] ArrayRefTest/10.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/10.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/10.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/10.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/10.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/10.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/10.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/10.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/10.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/10.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/10 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/11, where TypeParam = gmx::ArrayRef<unsigned char const>
3: [ RUN ] ArrayRefTest/11.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/11.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/11.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/11.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/11.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/11.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/11.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/11.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/11.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/11.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/11 (1 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/12, where TypeParam = gmx::ArrayRef<int const>
3: [ RUN ] ArrayRefTest/12.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/12.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/12.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/12.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/12.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/12.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/12.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/12.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/12.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/12.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/12 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/13, where TypeParam = gmx::ArrayRef<unsigned int const>
3: [ RUN ] ArrayRefTest/13.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/13.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/13.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/13.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/13.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/13.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/13.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/13.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/13.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/13.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/13 (1 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/14, where TypeParam = gmx::ArrayRef<long const>
3: [ RUN ] ArrayRefTest/14.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/14.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/14.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/14.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/14.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/14.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/14.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/14.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/14.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/14.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/14 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/15, where TypeParam = gmx::ArrayRef<unsigned long const>
3: [ RUN ] ArrayRefTest/15.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/15.MakeWithAssignmentWorks (1 ms)
3: [ RUN ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/15.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/15.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/15.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/15.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/15.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/15.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/15.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/15.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/15 (1 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/16, where TypeParam = gmx::ArrayRef<long long const>
3: [ RUN ] ArrayRefTest/16.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/16.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/16.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/16.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/16.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/16.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/16.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/16.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/16.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/16.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/16 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/17, where TypeParam = gmx::ArrayRef<unsigned long long const>
3: [ RUN ] ArrayRefTest/17.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/17.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/17.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/17.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/17.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/17.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/17.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/17.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/17.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/17.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/17 (1 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/18, where TypeParam = gmx::ArrayRef<float const>
3: [ RUN ] ArrayRefTest/18.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/18.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/18.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/18.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/18.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/18.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/18.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/18.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/18.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/18.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/18 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/19, where TypeParam = gmx::ArrayRef<double const>
3: [ RUN ] ArrayRefTest/19.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/19.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/19.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/19.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/19.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/19.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/19.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/19.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/19.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/19.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/19 (1 ms total)
3:
3: [----------] 2 tests from CStringUtilityTest
3: [ RUN ] CStringUtilityTest.CaseInsensitiveComparison
3: [ OK ] CStringUtilityTest.CaseInsensitiveComparison (0 ms)
3: [ RUN ] CStringUtilityTest.CaseInsensitiveComparisonInLength
3: [ OK ] CStringUtilityTest.CaseInsensitiveComparisonInLength (0 ms)
3: [----------] 2 tests from CStringUtilityTest (0 ms total)
3:
3: [----------] 2 tests from DefaultInitializationAllocator
3: [ RUN ] DefaultInitializationAllocator.PerformsValueInitialization
3: [ OK ] DefaultInitializationAllocator.PerformsValueInitialization (0 ms)
3: [ RUN ] DefaultInitializationAllocator.PerformsNoInitialization
3: [ OK ] DefaultInitializationAllocator.PerformsNoInitialization (0 ms)
3: [----------] 2 tests from DefaultInitializationAllocator (0 ms total)
3:
3: [----------] 4 tests from EnumerationHelpersTest
3: [ RUN ] EnumerationHelpersTest.EnumerationWrapperWorks
3: [ OK ] EnumerationHelpersTest.EnumerationWrapperWorks (0 ms)
3: [ RUN ] EnumerationHelpersTest.EnumerationArrayWorks
3: [ OK ] EnumerationHelpersTest.EnumerationArrayWorks (0 ms)
3: [ RUN ] EnumerationHelpersTest.EnumerationArrayCountIsSafe
3: [ OK ] EnumerationHelpersTest.EnumerationArrayCountIsSafe (0 ms)
3: [ RUN ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks
3: [ OK ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks (0 ms)
3: [----------] 4 tests from EnumerationHelpersTest (0 ms total)
3:
3: [----------] 9 tests from FixedCapacityVectorTest
3: [ RUN ] FixedCapacityVectorTest.IsEmpty
3: [ OK ] FixedCapacityVectorTest.IsEmpty (0 ms)
3: [ RUN ] FixedCapacityVectorTest.PushWorks
3: [ OK ] FixedCapacityVectorTest.PushWorks (0 ms)
3: [ RUN ] FixedCapacityVectorTest.PopWorks
3: [ OK ] FixedCapacityVectorTest.PopWorks (0 ms)
3: [ RUN ] FixedCapacityVectorTest.ClearWorks
3: [ OK ] FixedCapacityVectorTest.ClearWorks (0 ms)
3: [ RUN ] FixedCapacityVectorTest.EmplaceBackWorks
3: [ OK ] FixedCapacityVectorTest.EmplaceBackWorks (0 ms)
3: [ RUN ] FixedCapacityVectorTest.AtThrows
3: [ OK ] FixedCapacityVectorTest.AtThrows (0 ms)
3: [ RUN ] FixedCapacityVectorTest.IteratorWorks
3: [ OK ] FixedCapacityVectorTest.IteratorWorks (0 ms)
3: [ RUN ] FixedCapacityVectorTest.ReverseIteratorWorks
3: [ OK ] FixedCapacityVectorTest.ReverseIteratorWorks (0 ms)
3: [ RUN ] FixedCapacityVectorTest.ZeroCapacityWorks
3: [ OK ] FixedCapacityVectorTest.ZeroCapacityWorks (0 ms)
3: [----------] 9 tests from FixedCapacityVectorTest (1 ms total)
3:
3: [----------] 5 tests from InMemorySerializerTest
3: [ RUN ] InMemorySerializerTest.Roundtrip
3: [ OK ] InMemorySerializerTest.Roundtrip (0 ms)
3: [ RUN ] InMemorySerializerTest.RoundtripWithEndianessSwap
3: [ OK ] InMemorySerializerTest.RoundtripWithEndianessSwap (0 ms)
3: [ RUN ] InMemorySerializerTest.SerializerExplicitEndianessSwap
3: [ OK ] InMemorySerializerTest.SerializerExplicitEndianessSwap (0 ms)
3: [ RUN ] InMemorySerializerTest.DeserializerExplicitEndianessSwap
3: [ OK ] InMemorySerializerTest.DeserializerExplicitEndianessSwap (0 ms)
3: [ RUN ] InMemorySerializerTest.SizeIsCorrect
3: [ OK ] InMemorySerializerTest.SizeIsCorrect (0 ms)
3: [----------] 5 tests from InMemorySerializerTest (0 ms total)
3:
3: [----------] 4 tests from KeyValueTreeSerializerTest
3: [ RUN ] KeyValueTreeSerializerTest.EmptyTree
3: [ OK ] KeyValueTreeSerializerTest.EmptyTree (16 ms)
3: [ RUN ] KeyValueTreeSerializerTest.SimpleObject
3: [ OK ] KeyValueTreeSerializerTest.SimpleObject (2 ms)
3: [ RUN ] KeyValueTreeSerializerTest.ObjectWithArrays
3: [ OK ] KeyValueTreeSerializerTest.ObjectWithArrays (3 ms)
3: [ RUN ] KeyValueTreeSerializerTest.ObjectWithObjects
3: [ OK ] KeyValueTreeSerializerTest.ObjectWithObjects (0 ms)
3: [----------] 4 tests from KeyValueTreeSerializerTest (22 ms total)
3:
3: [----------] 6 tests from TreeValueTransformTest
3: [ RUN ] TreeValueTransformTest.SimpleTransforms
3: [ OK ] TreeValueTransformTest.SimpleTransforms (1 ms)
3: [ RUN ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive
3: [ OK ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive (2 ms)
3: [ RUN ] TreeValueTransformTest.SimpleTransformsToObject
3: [ OK ] TreeValueTransformTest.SimpleTransformsToObject (1 ms)
3: [ RUN ] TreeValueTransformTest.ObjectFromString
3: [ OK ] TreeValueTransformTest.ObjectFromString (1 ms)
3: [ RUN ] TreeValueTransformTest.ObjectFromMultipleStrings
3: [ OK ] TreeValueTransformTest.ObjectFromMultipleStrings (1 ms)
3: [ RUN ] TreeValueTransformTest.ScopedTransformRules
3: [ OK ] TreeValueTransformTest.ScopedTransformRules (1 ms)
3: [----------] 6 tests from TreeValueTransformTest (7 ms total)
3:
3: [----------] 1 test from TreeValueTransformErrorTest
3: [ RUN ] TreeValueTransformErrorTest.ConversionError
3: [ OK ] TreeValueTransformErrorTest.ConversionError (0 ms)
3: [----------] 1 test from TreeValueTransformErrorTest (1 ms total)
3:
3: [----------] 7 tests from LoggerTest
3: [ RUN ] LoggerTest.EmptyLoggerWorks
3: [ OK ] LoggerTest.EmptyLoggerWorks (0 ms)
3: [ RUN ] LoggerTest.LogsToStream
3: [ OK ] LoggerTest.LogsToStream (1 ms)
3: [ RUN ] LoggerTest.LogsToFile
3: [ OK ] LoggerTest.LogsToFile (2 ms)
3: [ RUN ] LoggerTest.LevelFilteringWorks
3: [ OK ] LoggerTest.LevelFilteringWorks (1 ms)
3: [ RUN ] LoggerTest.LogsToMultipleStreams
3: [ OK ] LoggerTest.LogsToMultipleStreams (0 ms)
3: [ RUN ] LoggerTest.LogsToMultipleFiles
3: [ OK ] LoggerTest.LogsToMultipleFiles (5 ms)
3: [ RUN ] LoggerTest.LogsToStreamAndFile
3: [ OK ] LoggerTest.LogsToStreamAndFile (1 ms)
3: [----------] 7 tests from LoggerTest (12 ms total)
3:
3: [----------] 4 tests from MutexBasicTest
3: [ RUN ] MutexBasicTest.CanBeMade
3: [ OK ] MutexBasicTest.CanBeMade (0 ms)
3: [ RUN ] MutexBasicTest.CanBeLocked
3: [ OK ] MutexBasicTest.CanBeLocked (0 ms)
3: [ RUN ] MutexBasicTest.CanBeTryLocked
3: [ OK ] MutexBasicTest.CanBeTryLocked (0 ms)
3: [ RUN ] MutexBasicTest.CanBeUsedInLockGuard
3: [ OK ] MutexBasicTest.CanBeUsedInLockGuard (0 ms)
3: [----------] 4 tests from MutexBasicTest (1 ms total)
3:
3: [----------] 3 tests from MutexTaskTest
3: [ RUN ] MutexTaskTest.MutualExclusionWorksWithLock
3: [ OK ] MutexTaskTest.MutualExclusionWorksWithLock (1 ms)
3: [ RUN ] MutexTaskTest.MutualExclusionWorksWithTryLockOnOtherThread
3: [ OK ] MutexTaskTest.MutualExclusionWorksWithTryLockOnOtherThread (1 ms)
3: [ RUN ] MutexTaskTest.MutualExclusionWorksWithTryLockOnSameThread
3: [ OK ] MutexTaskTest.MutualExclusionWorksWithTryLockOnSameThread (0 ms)
3: [----------] 3 tests from MutexTaskTest (2 ms total)
3:
3: [----------] 2 tests from PathTest
3: [ RUN ] PathTest.StripSourcePrefixWorks
3: [ OK ] PathTest.StripSourcePrefixWorks (0 ms)
3: [ RUN ] PathTest.SearchOperationsWork
3: [ OK ] PathTest.SearchOperationsWork (14 ms)
3: [----------] 2 tests from PathTest (16 ms total)
3:
3: [----------] 2 tests from PhysicalNodeCommunicatorTest
3: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct
3: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (0 ms)
3: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier
3: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms)
3: [----------] 2 tests from PhysicalNodeCommunicatorTest (0 ms total)
3:
3: [----------] 9 tests from StringUtilityTest
3: [ RUN ] StringUtilityTest.StartsWith
3: [ OK ] StringUtilityTest.StartsWith (0 ms)
3: [ RUN ] StringUtilityTest.EndsWith
3: [ OK ] StringUtilityTest.EndsWith (0 ms)
3: [ RUN ] StringUtilityTest.StripSuffixIfPresent
3: [ OK ] StringUtilityTest.StripSuffixIfPresent (1 ms)
3: [ RUN ] StringUtilityTest.StripString
3: [ OK ] StringUtilityTest.StripString (0 ms)
3: [ RUN ] StringUtilityTest.SplitString
3: [ OK ] StringUtilityTest.SplitString (1 ms)
3: [ RUN ] StringUtilityTest.SplitDelimitedString
3: [ OK ] StringUtilityTest.SplitDelimitedString (0 ms)
3: [ RUN ] StringUtilityTest.SplitAndTrimDelimitedString
3: [ OK ] StringUtilityTest.SplitAndTrimDelimitedString (1 ms)
3: [ RUN ] StringUtilityTest.CanCompareCaseInsensitive
3: [ OK ] StringUtilityTest.CanCompareCaseInsensitive (0 ms)
3: [ RUN ] StringUtilityTest.CanCompareCaseInsensitiveInLength
3: [ OK ] StringUtilityTest.CanCompareCaseInsensitiveInLength (0 ms)
3: [----------] 9 tests from StringUtilityTest (4 ms total)
3:
3: [----------] 2 tests from FormatStringTest
3: [ RUN ] FormatStringTest.HandlesBasicFormatting
3: [ OK ] FormatStringTest.HandlesBasicFormatting (0 ms)
3: [ RUN ] FormatStringTest.HandlesLongStrings
3: [ OK ] FormatStringTest.HandlesLongStrings (0 ms)
3: [----------] 2 tests from FormatStringTest (0 ms total)
3:
3: [----------] 1 test from StringFormatterTest
3: [ RUN ] StringFormatterTest.HandlesBasicFormatting
3: [ OK ] StringFormatterTest.HandlesBasicFormatting (0 ms)
3: [----------] 1 test from StringFormatterTest (0 ms total)
3:
3: [----------] 1 test from formatAndJoinTest
3: [ RUN ] formatAndJoinTest.Works
3: [ OK ] formatAndJoinTest.Works (0 ms)
3: [----------] 1 test from formatAndJoinTest (0 ms total)
3:
3: [----------] 1 test from JoinStringsTest
3: [ RUN ] JoinStringsTest.Works
3: [ OK ] JoinStringsTest.Works (0 ms)
3: [----------] 1 test from JoinStringsTest (0 ms total)
3:
3: [----------] 6 tests from ReplaceAllTest
3: [ RUN ] ReplaceAllTest.HandlesEmptyStrings
3: [ OK ] ReplaceAllTest.HandlesEmptyStrings (0 ms)
3: [ RUN ] ReplaceAllTest.HandlesNoMatches
3: [ OK ] ReplaceAllTest.HandlesNoMatches (0 ms)
3: [ RUN ] ReplaceAllTest.HandlesMatchesAtEnds
3: [ OK ] ReplaceAllTest.HandlesMatchesAtEnds (0 ms)
3: [ RUN ] ReplaceAllTest.HandlesMultipleMatches
3: [ OK ] ReplaceAllTest.HandlesMultipleMatches (0 ms)
3: [ RUN ] ReplaceAllTest.HandlesWordBoundaries
3: [ OK ] ReplaceAllTest.HandlesWordBoundaries (0 ms)
3: [ RUN ] ReplaceAllTest.HandlesPossibleRecursiveMatches
3: [ OK ] ReplaceAllTest.HandlesPossibleRecursiveMatches (0 ms)
3: [----------] 6 tests from ReplaceAllTest (2 ms total)
3:
3: [----------] 10 tests from TextLineWrapperTest
3: [ RUN ] TextLineWrapperTest.HandlesEmptyStrings
3: [ OK ] TextLineWrapperTest.HandlesEmptyStrings (0 ms)
3: [ RUN ] TextLineWrapperTest.HandlesTrailingWhitespace
3: [ OK ] TextLineWrapperTest.HandlesTrailingWhitespace (1 ms)
3: [ RUN ] TextLineWrapperTest.HandlesTrailingNewlines
3: [ OK ] TextLineWrapperTest.HandlesTrailingNewlines (0 ms)
3: [ RUN ] TextLineWrapperTest.WrapsCorrectly
3: [ OK ] TextLineWrapperTest.WrapsCorrectly (1 ms)
3: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks
3: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks (1 ms)
3: [ RUN ] TextLineWrapperTest.HandlesIndent
3: [ OK ] TextLineWrapperTest.HandlesIndent (1 ms)
3: [ RUN ] TextLineWrapperTest.HandlesIndentWithEmptyLines
3: [ OK ] TextLineWrapperTest.HandlesIndentWithEmptyLines (0 ms)
3: [ RUN ] TextLineWrapperTest.HandlesHangingIndent
3: [ OK ] TextLineWrapperTest.HandlesHangingIndent (0 ms)
3: [ RUN ] TextLineWrapperTest.HandlesContinuationCharacter
3: [ OK ] TextLineWrapperTest.HandlesContinuationCharacter (1 ms)
3: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace
3: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace (0 ms)
3: [----------] 10 tests from TextLineWrapperTest (7 ms total)
3:
3: [----------] 6 tests from TextWriterTest
3: [ RUN ] TextWriterTest.WritesLines
3: [ OK ] TextWriterTest.WritesLines (0 ms)
3: [ RUN ] TextWriterTest.WritesLinesInParts
3: [ OK ] TextWriterTest.WritesLinesInParts (0 ms)
3: [ RUN ] TextWriterTest.WritesWrappedLines
3: [ OK ] TextWriterTest.WritesWrappedLines (1 ms)
3: [ RUN ] TextWriterTest.WritesLinesInPartsWithWrapper
3: [ OK ] TextWriterTest.WritesLinesInPartsWithWrapper (1 ms)
3: [ RUN ] TextWriterTest.TracksNewlines
3: [ OK ] TextWriterTest.TracksNewlines (0 ms)
3: [ RUN ] TextWriterTest.PreservesTrailingWhitespace
3: [ OK ] TextWriterTest.PreservesTrailingWhitespace (1 ms)
3: [----------] 6 tests from TextWriterTest (4 ms total)
3:
3: [----------] 1 test from TypeTraitsTest
3: [ RUN ] TypeTraitsTest.IsIntegralConstant
3: [ OK ] TypeTraitsTest.IsIntegralConstant (0 ms)
3: [----------] 1 test from TypeTraitsTest (1 ms total)
3:
3: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32
3: [ RUN ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0
3: [ OK ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 (0 ms)
3: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitBit/0
3: [ OK ] BitmaskTest32_11/BitmaskTest32.InitBit/0 (0 ms)
3: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0
3: [ OK ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 (0 ms)
3: [ RUN ] BitmaskTest32_11/BitmaskTest32.Disjoint/0
3: [ OK ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 (0 ms)
3: [ RUN ] BitmaskTest32_11/BitmaskTest32.Union/0
3: [ OK ] BitmaskTest32_11/BitmaskTest32.Union/0 (0 ms)
3: [ RUN ] BitmaskTest32_11/BitmaskTest32.ToHex/0
3: [ OK ] BitmaskTest32_11/BitmaskTest32.ToHex/0 (0 ms)
3: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 (1 ms total)
3:
3: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/0
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/0 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/1
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/1 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 (0 ms)
3: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 (3 ms total)
3:
3: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/0
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/0 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/1
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/1 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 (0 ms)
3: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 (3 ms total)
3:
3: [----------] 9 tests from WithAndWithoutMutex/DifferentTasksTest
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/0
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/0 (1 ms)
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/1
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/1 (0 ms)
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/2
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/2 (1 ms)
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/0
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/0 (0 ms)
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/1
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/1 (0 ms)
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/2
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/2 (0 ms)
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/0
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/0 (0 ms)
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/1
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/1 (0 ms)
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/2
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/2 (0 ms)
3: [----------] 9 tests from WithAndWithoutMutex/DifferentTasksTest (4 ms total)
3:
3: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest
3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0
3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 (0 ms)
3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1
3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 (0 ms)
3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2
3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 (1 ms)
3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3
3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 (0 ms)
3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4
3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 (1 ms)
3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5
3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 (0 ms)
3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6
3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 (1 ms)
3: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest (4 ms total)
3:
3: [----------] Global test environment tear-down
3: [==========] 347 tests from 56 test cases ran. (120 ms total)
3: [ PASSED ] 347 tests.
3/52 Test #3: UtilityUnitTests .................... Passed 0.24 sec
test 4
Start 4: UtilityMpiUnitTests
4: Test command: /<<PKGBUILDDIR>>/build/basic/bin/utility-mpi-test "-ntmpi" "4" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/UtilityMpiUnitTests.xml"
4: Test timeout computed to be: 30
4: [==========] Running 2 tests from 1 test case.
4: [----------] Global test environment set-up.
4: [----------] 2 tests from PhysicalNodeCommunicatorTest
4: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct
4: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (3 ms)
4: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier
4: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (1 ms)
4: [----------] 2 tests from PhysicalNodeCommunicatorTest (4 ms total)
4:
4: [----------] Global test environment tear-down
4: [==========] 2 tests from 1 test case ran. (4 ms total)
4: [ PASSED ] 2 tests.
4/52 Test #4: UtilityMpiUnitTests ................. Passed 0.07 sec
test 5
Start 5: MdlibUnitTest
5: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdlib-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdlibUnitTest.xml"
5: Test timeout computed to be: 30
5: [==========] Running 149 tests from 11 test cases.
5: [----------] Global test environment set-up.
5: [----------] 1 test from VerletBufferConstraintTest
5: [ RUN ] VerletBufferConstraintTest.EqualMasses
5: [ OK ] VerletBufferConstraintTest.EqualMasses (0 ms)
5: [----------] 1 test from VerletBufferConstraintTest (0 ms total)
5:
5: [----------] 2 tests from PrEbinTest
5: [ RUN ] PrEbinTest.HandlesAverages
5: [ OK ] PrEbinTest.HandlesAverages (2 ms)
5: [ RUN ] PrEbinTest.HandlesEmptyAverages
5: [ OK ] PrEbinTest.HandlesEmptyAverages (15 ms)
5: [----------] 2 tests from PrEbinTest (17 ms total)
5:
5: [----------] 4 tests from ShakeTest
5: [ RUN ] ShakeTest.ConstrainsOneBond
5: [ OK ] ShakeTest.ConstrainsOneBond (0 ms)
5: [ RUN ] ShakeTest.ConstrainsTwoDisjointBonds
5: [ OK ] ShakeTest.ConstrainsTwoDisjointBonds (0 ms)
5: [ RUN ] ShakeTest.ConstrainsTwoBondsWithACommonAtom
5: [ OK ] ShakeTest.ConstrainsTwoBondsWithACommonAtom (1 ms)
5: [ RUN ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms
5: [ OK ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms (0 ms)
5: [----------] 4 tests from ShakeTest (1 ms total)
5:
5: [----------] 1 test from NullSignalTest
5: [ RUN ] NullSignalTest.NullSignallerWorks
5: [ OK ] NullSignalTest.NullSignallerWorks (0 ms)
5: [----------] 1 test from NullSignalTest (0 ms total)
5:
5: [----------] 7 tests from SignalTest
5: [ RUN ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace
5: [ OK ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace (0 ms)
5: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace
5: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace (0 ms)
5: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace
5: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace (0 ms)
5: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace
5: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace (0 ms)
5: [ RUN ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace
5: [ OK ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace (0 ms)
5: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace
5: [ OK ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace (0 ms)
5: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace
5: [ OK ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace (0 ms)
5: [----------] 7 tests from SignalTest (1 ms total)
5:
5: [----------] 9 tests from UpdateGroups
5: [ RUN ] UpdateGroups.ethaneUA
5: [ OK ] UpdateGroups.ethaneUA (1 ms)
5: [ RUN ] UpdateGroups.methane
5: [ OK ] UpdateGroups.methane (0 ms)
5: [ RUN ] UpdateGroups.ethane
5: [ OK ] UpdateGroups.ethane (1 ms)
5: [ RUN ] UpdateGroups.butaneUA
5: [ OK ] UpdateGroups.butaneUA (0 ms)
5: [ RUN ] UpdateGroups.waterThreeSite
5: [ OK ] UpdateGroups.waterThreeSite (0 ms)
5: [ RUN ] UpdateGroups.waterFourSite
5: [ OK ] UpdateGroups.waterFourSite (0 ms)
5: [ RUN ] UpdateGroups.fourAtomsWithSettle
5: [ OK ] UpdateGroups.fourAtomsWithSettle (1 ms)
5: [ RUN ] UpdateGroups.waterFlexAngle
5: [ OK ] UpdateGroups.waterFlexAngle (0 ms)
5: [ RUN ] UpdateGroups.twoMoltypes
5: [ OK ] UpdateGroups.twoMoltypes (0 ms)
5: [----------] 9 tests from UpdateGroups (3 ms total)
5:
5: [----------] 1 test from UpdateGroupsCog
5: [ RUN ] UpdateGroupsCog.ComputesCogs
5: [ OK ] UpdateGroupsCog.ComputesCogs (9 ms)
5: [----------] 1 test from UpdateGroupsCog (10 ms total)
5:
5: [----------] 84 tests from WithParameters/ConstraintsTest
5: [ RUN ] WithParameters/ConstraintsTest.SingleConstraint/0
5: [ OK ] WithParameters/ConstraintsTest.SingleConstraint/0 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.SingleConstraint/1
5: [ OK ] WithParameters/ConstraintsTest.SingleConstraint/1 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.SingleConstraint/2
5: [ OK ] WithParameters/ConstraintsTest.SingleConstraint/2 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.SingleConstraint/3
5: [ OK ] WithParameters/ConstraintsTest.SingleConstraint/3 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/0
5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/0 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/1
5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/1 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/2
5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/2 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/3
5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/3 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/4
5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/4 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/5
5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/5 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/6
5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/6 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/7
5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/7 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/0
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/0 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/1
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/1 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/2
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/2 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/3
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/3 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/4
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/4 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/5
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/5 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/6
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/6 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/7
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/7 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/8
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/8 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/9
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/9 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/10
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/10 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/11
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/11 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/0
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/0 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/1
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/1 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/2
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/2 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/3
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/3 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/4
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/4 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/5
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/5 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/6
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/6 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/7
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/7 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/8
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/8 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/9
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/9 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/10
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/10 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/11
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/11 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/12
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/12 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/13
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/13 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/14
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/14 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/15
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/15 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/0
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/0 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/1
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/1 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/2
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/2 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/3
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/3 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/4
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/4 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/5
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/5 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/6
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/6 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/7
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/7 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/8
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/8 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/9
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/9 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/10
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/10 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/11
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/11 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/12
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/12 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/13
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/13 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/14
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/14 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/15
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/15 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/16
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/16 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/17
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/17 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/18
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/18 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/19
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/19 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/0
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/0 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/1
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/1 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/2
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/2 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/3
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/3 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/4
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/4 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/5
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/5 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/6
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/6 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/7
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/7 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/8
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/8 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/9
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/9 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/10
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/10 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/11
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/11 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/12
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/12 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/13
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/13 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/14
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/14 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/15
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/15 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/16
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/16 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/17
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/17 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/18
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/18 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/19
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/19 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/20
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/20 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/21
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/21 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/22
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/22 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/23
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/23 (0 ms)
5: [----------] 84 tests from WithParameters/ConstraintsTest (35 ms total)
5:
5: [----------] 11 tests from WithParameters/EnergyOutputTest
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/0
5: Opened /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_0.edr as single precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/0 (24 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/1
5: Opened /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_1.edr as single precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/1 (18 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/2
5: Opened /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_2.edr as single precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/2 (28 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/3
5: [ OK ] WithParameters/EnergyOutputTest.CheckOutput/3 (3 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/4
5: Opened /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_4.edr as single precision energy file
5:
Reading energy frame 0 time 10.100
Reading energy frame 1 time 27.500
Reading energy frame 2 time 44.900
Reading energy frame 3 time 62.300
Reading energy frame 4 time 79.700
Reading energy frame 5 time 97.100
Reading energy frame 6 time 114.500
Reading energy frame 7 time 131.900
Reading energy frame 8 time 149.300
Reading energy frame 9 time 166.700 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/4 (78 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/5
5: Opened /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_5.edr as single precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/5 (15 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/6
5: Opened /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_6.edr as single precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/6 (13 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/7
5: Opened /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_7.edr as single precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/7 (14 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/8
5: Opened /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_8.edr as single precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/8 (13 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/9
5: Opened /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_9.edr as single precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/9 (13 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/10
5: Opened /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_10.edr as single precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/10 (14 ms)
5: [----------] 11 tests from WithParameters/EnergyOutputTest (259 ms total)
5:
5: [----------] 16 tests from WithParameters/LeapFrogTest
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/0
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/0 (1 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/1
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/1 (0 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/2
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/2 (0 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/3
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/3 (1 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/4
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/4 (2 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/5
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/5 (12 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/6
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/6 (32 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/7
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/7 (2 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/8
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/8 (1 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/9
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/9 (1 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/10
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/10 (12 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/11
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/11 (11 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/12
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/12 (11 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/13
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/13 (12 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/14
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/14 (12 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/15
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/15 (12 ms)
5: [----------] 16 tests from WithParameters/LeapFrogTest (147 ms total)
5:
5: [----------] 13 tests from WithParameters/SettleTest
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/0
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/0 (2 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/1
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/1 (1 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/2
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/2 (2 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/3
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/3 (2 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/4
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/4 (2 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/5
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/5 (2 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/6
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/6 (3 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/7
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/7 (4 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/8
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/8 (7 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/9
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/9 (4 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/10
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/10 (4 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/11
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/11 (8 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/12
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/12 (8 ms)
5: [----------] 13 tests from WithParameters/SettleTest (60 ms total)
5:
5: [----------] Global test environment tear-down
5: [==========] 149 tests from 11 test cases ran. (535 ms total)
5: [ PASSED ] 149 tests.
5/52 Test #5: MdlibUnitTest ....................... Passed 0.63 sec
test 6
Start 6: AppliedForcesUnitTest
6: Test command: /<<PKGBUILDDIR>>/build/basic/bin/applied_forces-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/AppliedForcesUnitTest.xml"
6: Test timeout computed to be: 30
6: [==========] Running 20 tests from 4 test cases.
6: [----------] Global test environment set-up.
6: [----------] 2 tests from DensityFittingTest
6: [ RUN ] DensityFittingTest.ForceProviderLackingInputThrows
6: [ OK ] DensityFittingTest.ForceProviderLackingInputThrows (4 ms)
6: [ RUN ] DensityFittingTest.SingleAtom
6: [ OK ] DensityFittingTest.SingleAtom (16 ms)
6: [----------] 2 tests from DensityFittingTest (20 ms total)
6:
6: [----------] 8 tests from DensityFittingOptionsTest
6: [ RUN ] DensityFittingOptionsTest.DefaultParameters
6: [ OK ] DensityFittingOptionsTest.DefaultParameters (0 ms)
6: [ RUN ] DensityFittingOptionsTest.OptionSetsActive
6: [ OK ] DensityFittingOptionsTest.OptionSetsActive (1 ms)
6: [ RUN ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive
6: [ OK ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive (1 ms)
6: [ RUN ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive
6: [ OK ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive (1 ms)
6: [ RUN ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup
6: [ OK ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup (2 ms)
6: [ RUN ] DensityFittingOptionsTest.InternalsToKvt
6: [ OK ] DensityFittingOptionsTest.InternalsToKvt (0 ms)
6: [ RUN ] DensityFittingOptionsTest.KvtToInternal
6: [ OK ] DensityFittingOptionsTest.KvtToInternal (1 ms)
6: [ RUN ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent
6: [ OK ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent (1 ms)
6: [----------] 8 tests from DensityFittingOptionsTest (7 ms total)
6:
6: [----------] 7 tests from DensityFittingAmplitudeLookupTest
6: [ RUN ] DensityFittingAmplitudeLookupTest.Unity
6: [ OK ] DensityFittingAmplitudeLookupTest.Unity (0 ms)
6: [ RUN ] DensityFittingAmplitudeLookupTest.Charge
6: [ OK ] DensityFittingAmplitudeLookupTest.Charge (0 ms)
6: [ RUN ] DensityFittingAmplitudeLookupTest.Masses
6: [ OK ] DensityFittingAmplitudeLookupTest.Masses (0 ms)
6: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyAssign
6: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyAssign (0 ms)
6: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyConstruct
6: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyConstruct (0 ms)
6: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveAssign
6: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveAssign (0 ms)
6: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveConstruct
6: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveConstruct (0 ms)
6: [----------] 7 tests from DensityFittingAmplitudeLookupTest (0 ms total)
6:
6: [----------] 3 tests from ElectricFieldTest
6: [ RUN ] ElectricFieldTest.Static
6: [ OK ] ElectricFieldTest.Static (0 ms)
6: [ RUN ] ElectricFieldTest.Oscillating
6: [ OK ] ElectricFieldTest.Oscillating (2 ms)
6: [ RUN ] ElectricFieldTest.Pulsed
6: [ OK ] ElectricFieldTest.Pulsed (0 ms)
6: [----------] 3 tests from ElectricFieldTest (2 ms total)
6:
6: [----------] Global test environment tear-down
6: [==========] 20 tests from 4 test cases ran. (31 ms total)
6: [ PASSED ] 20 tests.
6/52 Test #6: AppliedForcesUnitTest ............... Passed 0.09 sec
test 7
Start 7: ListedForcesTest
7: Test command: /<<PKGBUILDDIR>>/build/basic/bin/listed_forces-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/ListedForcesTest.xml"
7: Test timeout computed to be: 30
7: [==========] Running 315 tests from 5 test cases.
7: [----------] Global test environment set-up.
7: [----------] 72 tests from Bond/ListedForcesTest
7: [ RUN ] Bond/ListedForcesTest.Ifunc/0
7: [ OK ] Bond/ListedForcesTest.Ifunc/0 (27 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/1
7: [ OK ] Bond/ListedForcesTest.Ifunc/1 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/2
7: [ OK ] Bond/ListedForcesTest.Ifunc/2 (2 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/3
7: [ OK ] Bond/ListedForcesTest.Ifunc/3 (4 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/4
7: [ OK ] Bond/ListedForcesTest.Ifunc/4 (11 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/5
7: [ OK ] Bond/ListedForcesTest.Ifunc/5 (2 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/6
7: [ OK ] Bond/ListedForcesTest.Ifunc/6 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/7
7: [ OK ] Bond/ListedForcesTest.Ifunc/7 (12 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/8
7: [ OK ] Bond/ListedForcesTest.Ifunc/8 (2 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/9
7: [ OK ] Bond/ListedForcesTest.Ifunc/9 (15 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/10
7: [ OK ] Bond/ListedForcesTest.Ifunc/10 (9 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/11
7: [ OK ] Bond/ListedForcesTest.Ifunc/11 (3 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/12
7: [ OK ] Bond/ListedForcesTest.Ifunc/12 (3 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/13
7: [ OK ] Bond/ListedForcesTest.Ifunc/13 (3 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/14
7: [ OK ] Bond/ListedForcesTest.Ifunc/14 (2 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/15
7: [ OK ] Bond/ListedForcesTest.Ifunc/15 (2 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/16
7: [ OK ] Bond/ListedForcesTest.Ifunc/16 (3 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/17
7: [ OK ] Bond/ListedForcesTest.Ifunc/17 (3 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/18
7: [ OK ] Bond/ListedForcesTest.Ifunc/18 (2 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/19
7: [ OK ] Bond/ListedForcesTest.Ifunc/19 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/20
7: [ OK ] Bond/ListedForcesTest.Ifunc/20 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/21
7: [ OK ] Bond/ListedForcesTest.Ifunc/21 (2 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/22
7: [ OK ] Bond/ListedForcesTest.Ifunc/22 (2 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/23
7: [ OK ] Bond/ListedForcesTest.Ifunc/23 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/24
7: [ OK ] Bond/ListedForcesTest.Ifunc/24 (2 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/25
7: [ OK ] Bond/ListedForcesTest.Ifunc/25 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/26
7: [ OK ] Bond/ListedForcesTest.Ifunc/26 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/27
7: [ OK ] Bond/ListedForcesTest.Ifunc/27 (3 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/28
7: [ OK ] Bond/ListedForcesTest.Ifunc/28 (3 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/29
7: [ OK ] Bond/ListedForcesTest.Ifunc/29 (3 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/30
7: [ OK ] Bond/ListedForcesTest.Ifunc/30 (3 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/31
7: [ OK ] Bond/ListedForcesTest.Ifunc/31 (3 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/32
7: [ OK ] Bond/ListedForcesTest.Ifunc/32 (3 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/33
7: [ OK ] Bond/ListedForcesTest.Ifunc/33 (2 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/34
7: [ OK ] Bond/ListedForcesTest.Ifunc/34 (2 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/35
7: [ OK ] Bond/ListedForcesTest.Ifunc/35 (3 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/36
7: [ OK ] Bond/ListedForcesTest.Ifunc/36 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/37
7: [ OK ] Bond/ListedForcesTest.Ifunc/37 (2 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/38
7: [ OK ] Bond/ListedForcesTest.Ifunc/38 (2 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/39
7: [ OK ] Bond/ListedForcesTest.Ifunc/39 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/40
7: [ OK ] Bond/ListedForcesTest.Ifunc/40 (3 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/41
7: [ OK ] Bond/ListedForcesTest.Ifunc/41 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/42
7: [ OK ] Bond/ListedForcesTest.Ifunc/42 (2 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/43
7: [ OK ] Bond/ListedForcesTest.Ifunc/43 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/44
7: [ OK ] Bond/ListedForcesTest.Ifunc/44 (2 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/45
7: [ OK ] Bond/ListedForcesTest.Ifunc/45 (3 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/46
7: [ OK ] Bond/ListedForcesTest.Ifunc/46 (3 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/47
7: [ OK ] Bond/ListedForcesTest.Ifunc/47 (2 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/48
7: [ OK ] Bond/ListedForcesTest.Ifunc/48 (3 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/49
7: [ OK ] Bond/ListedForcesTest.Ifunc/49 (3 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/50
7: [ OK ] Bond/ListedForcesTest.Ifunc/50 (2 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/51
7: [ OK ] Bond/ListedForcesTest.Ifunc/51 (2 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/52
7: [ OK ] Bond/ListedForcesTest.Ifunc/52 (2 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/53
7: [ OK ] Bond/ListedForcesTest.Ifunc/53 (2 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/54
7: [ OK ] Bond/ListedForcesTest.Ifunc/54 (2 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/55
7: [ OK ] Bond/ListedForcesTest.Ifunc/55 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/56
7: [ OK ] Bond/ListedForcesTest.Ifunc/56 (2 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/57
7: [ OK ] Bond/ListedForcesTest.Ifunc/57 (2 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/58
7: [ OK ] Bond/ListedForcesTest.Ifunc/58 (2 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/59
7: [ OK ] Bond/ListedForcesTest.Ifunc/59 (2 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/60
7: [ OK ] Bond/ListedForcesTest.Ifunc/60 (2 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/61
7: [ OK ] Bond/ListedForcesTest.Ifunc/61 (2 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/62
7: [ OK ] Bond/ListedForcesTest.Ifunc/62 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/63
7: [ OK ] Bond/ListedForcesTest.Ifunc/63 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/64
7: [ OK ] Bond/ListedForcesTest.Ifunc/64 (2 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/65
7: [ OK ] Bond/ListedForcesTest.Ifunc/65 (2 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/66
7: [ OK ] Bond/ListedForcesTest.Ifunc/66 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/67
7: [ OK ] Bond/ListedForcesTest.Ifunc/67 (2 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/68
7: [ OK ] Bond/ListedForcesTest.Ifunc/68 (2 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/69
7: [ OK ] Bond/ListedForcesTest.Ifunc/69 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/70
7: [ OK ] Bond/ListedForcesTest.Ifunc/70 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/71
7: [ OK ] Bond/ListedForcesTest.Ifunc/71 (1 ms)
7: [----------] 72 tests from Bond/ListedForcesTest (221 ms total)
7:
7: [----------] 99 tests from Angle/ListedForcesTest
7: [ RUN ] Angle/ListedForcesTest.Ifunc/0
7: [ OK ] Angle/ListedForcesTest.Ifunc/0 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/1
7: [ OK ] Angle/ListedForcesTest.Ifunc/1 (0 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/2
7: [ OK ] Angle/ListedForcesTest.Ifunc/2 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/3
7: [ OK ] Angle/ListedForcesTest.Ifunc/3 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/4
7: [ OK ] Angle/ListedForcesTest.Ifunc/4 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/5
7: [ OK ] Angle/ListedForcesTest.Ifunc/5 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/6
7: [ OK ] Angle/ListedForcesTest.Ifunc/6 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/7
7: [ OK ] Angle/ListedForcesTest.Ifunc/7 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/8
7: [ OK ] Angle/ListedForcesTest.Ifunc/8 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/9
7: [ OK ] Angle/ListedForcesTest.Ifunc/9 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/10
7: [ OK ] Angle/ListedForcesTest.Ifunc/10 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/11
7: [ OK ] Angle/ListedForcesTest.Ifunc/11 (3 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/12
7: [ OK ] Angle/ListedForcesTest.Ifunc/12 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/13
7: [ OK ] Angle/ListedForcesTest.Ifunc/13 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/14
7: [ OK ] Angle/ListedForcesTest.Ifunc/14 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/15
7: [ OK ] Angle/ListedForcesTest.Ifunc/15 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/16
7: [ OK ] Angle/ListedForcesTest.Ifunc/16 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/17
7: [ OK ] Angle/ListedForcesTest.Ifunc/17 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/18
7: [ OK ] Angle/ListedForcesTest.Ifunc/18 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/19
7: [ OK ] Angle/ListedForcesTest.Ifunc/19 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/20
7: [ OK ] Angle/ListedForcesTest.Ifunc/20 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/21
7: [ OK ] Angle/ListedForcesTest.Ifunc/21 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/22
7: [ OK ] Angle/ListedForcesTest.Ifunc/22 (0 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/23
7: [ OK ] Angle/ListedForcesTest.Ifunc/23 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/24
7: [ OK ] Angle/ListedForcesTest.Ifunc/24 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/25
7: [ OK ] Angle/ListedForcesTest.Ifunc/25 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/26
7: [ OK ] Angle/ListedForcesTest.Ifunc/26 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/27
7: [ OK ] Angle/ListedForcesTest.Ifunc/27 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/28
7: [ OK ] Angle/ListedForcesTest.Ifunc/28 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/29
7: [ OK ] Angle/ListedForcesTest.Ifunc/29 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/30
7: [ OK ] Angle/ListedForcesTest.Ifunc/30 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/31
7: [ OK ] Angle/ListedForcesTest.Ifunc/31 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/32
7: [ OK ] Angle/ListedForcesTest.Ifunc/32 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/33
7: [ OK ] Angle/ListedForcesTest.Ifunc/33 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/34
7: [ OK ] Angle/ListedForcesTest.Ifunc/34 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/35
7: [ OK ] Angle/ListedForcesTest.Ifunc/35 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/36
7: [ OK ] Angle/ListedForcesTest.Ifunc/36 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/37
7: [ OK ] Angle/ListedForcesTest.Ifunc/37 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/38
7: [ OK ] Angle/ListedForcesTest.Ifunc/38 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/39
7: [ OK ] Angle/ListedForcesTest.Ifunc/39 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/40
7: [ OK ] Angle/ListedForcesTest.Ifunc/40 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/41
7: [ OK ] Angle/ListedForcesTest.Ifunc/41 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/42
7: [ OK ] Angle/ListedForcesTest.Ifunc/42 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/43
7: [ OK ] Angle/ListedForcesTest.Ifunc/43 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/44
7: [ OK ] Angle/ListedForcesTest.Ifunc/44 (0 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/45
7: [ OK ] Angle/ListedForcesTest.Ifunc/45 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/46
7: [ OK ] Angle/ListedForcesTest.Ifunc/46 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/47
7: [ OK ] Angle/ListedForcesTest.Ifunc/47 (8 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/48
7: [ OK ] Angle/ListedForcesTest.Ifunc/48 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/49
7: [ OK ] Angle/ListedForcesTest.Ifunc/49 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/50
7: [ OK ] Angle/ListedForcesTest.Ifunc/50 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/51
7: [ OK ] Angle/ListedForcesTest.Ifunc/51 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/52
7: [ OK ] Angle/ListedForcesTest.Ifunc/52 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/53
7: [ OK ] Angle/ListedForcesTest.Ifunc/53 (17 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/54
7: [ OK ] Angle/ListedForcesTest.Ifunc/54 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/55
7: [ OK ] Angle/ListedForcesTest.Ifunc/55 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/56
7: [ OK ] Angle/ListedForcesTest.Ifunc/56 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/57
7: [ OK ] Angle/ListedForcesTest.Ifunc/57 (11 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/58
7: [ OK ] Angle/ListedForcesTest.Ifunc/58 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/59
7: [ OK ] Angle/ListedForcesTest.Ifunc/59 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/60
7: [ OK ] Angle/ListedForcesTest.Ifunc/60 (0 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/61
7: [ OK ] Angle/ListedForcesTest.Ifunc/61 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/62
7: [ OK ] Angle/ListedForcesTest.Ifunc/62 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/63
7: [ OK ] Angle/ListedForcesTest.Ifunc/63 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/64
7: [ OK ] Angle/ListedForcesTest.Ifunc/64 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/65
7: [ OK ] Angle/ListedForcesTest.Ifunc/65 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/66
7: [ OK ] Angle/ListedForcesTest.Ifunc/66 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/67
7: [ OK ] Angle/ListedForcesTest.Ifunc/67 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/68
7: [ OK ] Angle/ListedForcesTest.Ifunc/68 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/69
7: [ OK ] Angle/ListedForcesTest.Ifunc/69 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/70
7: [ OK ] Angle/ListedForcesTest.Ifunc/70 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/71
7: [ OK ] Angle/ListedForcesTest.Ifunc/71 (0 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/72
7: [ OK ] Angle/ListedForcesTest.Ifunc/72 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/73
7: [ OK ] Angle/ListedForcesTest.Ifunc/73 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/74
7: [ OK ] Angle/ListedForcesTest.Ifunc/74 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/75
7: [ OK ] Angle/ListedForcesTest.Ifunc/75 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/76
7: [ OK ] Angle/ListedForcesTest.Ifunc/76 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/77
7: [ OK ] Angle/ListedForcesTest.Ifunc/77 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/78
7: [ OK ] Angle/ListedForcesTest.Ifunc/78 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/79
7: [ OK ] Angle/ListedForcesTest.Ifunc/79 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/80
7: [ OK ] Angle/ListedForcesTest.Ifunc/80 (0 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/81
7: [ OK ] Angle/ListedForcesTest.Ifunc/81 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/82
7: [ OK ] Angle/ListedForcesTest.Ifunc/82 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/83
7: [ OK ] Angle/ListedForcesTest.Ifunc/83 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/84
7: [ OK ] Angle/ListedForcesTest.Ifunc/84 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/85
7: [ OK ] Angle/ListedForcesTest.Ifunc/85 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/86
7: [ OK ] Angle/ListedForcesTest.Ifunc/86 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/87
7: [ OK ] Angle/ListedForcesTest.Ifunc/87 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/88
7: [ OK ] Angle/ListedForcesTest.Ifunc/88 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/89
7: [ OK ] Angle/ListedForcesTest.Ifunc/89 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/90
7: [ OK ] Angle/ListedForcesTest.Ifunc/90 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/91
7: [ OK ] Angle/ListedForcesTest.Ifunc/91 (0 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/92
7: [ OK ] Angle/ListedForcesTest.Ifunc/92 (0 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/93
7: [ OK ] Angle/ListedForcesTest.Ifunc/93 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/94
7: [ OK ] Angle/ListedForcesTest.Ifunc/94 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/95
7: [ OK ] Angle/ListedForcesTest.Ifunc/95 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/96
7: [ OK ] Angle/ListedForcesTest.Ifunc/96 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/97
7: [ OK ] Angle/ListedForcesTest.Ifunc/97 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/98
7: [ OK ] Angle/ListedForcesTest.Ifunc/98 (1 ms)
7: [----------] 99 tests from Angle/ListedForcesTest (178 ms total)
7:
7: [----------] 54 tests from Dihedral/ListedForcesTest
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/0
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/0 (2 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/1
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/1 (2 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/2
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/2 (2 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/3
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/3 (2 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/4
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/4 (2 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/5
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/5 (2 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/6
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/6 (2 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/7
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/7 (2 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/8
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/8 (2 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/9
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/9 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/10
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/10 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/11
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/11 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/12
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/12 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/13
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/13 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/14
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/14 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/15
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/15 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/16
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/16 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/17
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/17 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/18
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/18 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/19
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/19 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/20
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/20 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/21
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/21 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/22
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/22 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/23
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/23 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/24
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/24 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/25
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/25 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/26
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/26 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/27
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/27 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/28
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/28 (2 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/29
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/29 (2 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/30
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/30 (2 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/31
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/31 (2 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/32
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/32 (2 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/33
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/33 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/34
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/34 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/35
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/35 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/36
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/36 (2 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/37
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/37 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/38
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/38 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/39
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/39 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/40
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/40 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/41
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/41 (2 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/42
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/42 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/43
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/43 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/44
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/44 (2 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/45
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/45 (2 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/46
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/46 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/47
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/47 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/48
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/48 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/49
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/49 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/50
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/50 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/51
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/51 (0 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/52
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/52 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/53
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/53 (1 ms)
7: [----------] 54 tests from Dihedral/ListedForcesTest (80 ms total)
7:
7: [----------] 36 tests from Polarize/ListedForcesTest
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/0
7: [ OK ] Polarize/ListedForcesTest.Ifunc/0 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/1
7: [ OK ] Polarize/ListedForcesTest.Ifunc/1 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/2
7: [ OK ] Polarize/ListedForcesTest.Ifunc/2 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/3
7: [ OK ] Polarize/ListedForcesTest.Ifunc/3 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/4
7: [ OK ] Polarize/ListedForcesTest.Ifunc/4 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/5
7: [ OK ] Polarize/ListedForcesTest.Ifunc/5 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/6
7: [ OK ] Polarize/ListedForcesTest.Ifunc/6 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/7
7: [ OK ] Polarize/ListedForcesTest.Ifunc/7 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/8
7: [ OK ] Polarize/ListedForcesTest.Ifunc/8 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/9
7: [ OK ] Polarize/ListedForcesTest.Ifunc/9 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/10
7: [ OK ] Polarize/ListedForcesTest.Ifunc/10 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/11
7: [ OK ] Polarize/ListedForcesTest.Ifunc/11 (0 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/12
7: [ OK ] Polarize/ListedForcesTest.Ifunc/12 (0 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/13
7: [ OK ] Polarize/ListedForcesTest.Ifunc/13 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/14
7: [ OK ] Polarize/ListedForcesTest.Ifunc/14 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/15
7: [ OK ] Polarize/ListedForcesTest.Ifunc/15 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/16
7: [ OK ] Polarize/ListedForcesTest.Ifunc/16 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/17
7: [ OK ] Polarize/ListedForcesTest.Ifunc/17 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/18
7: [ OK ] Polarize/ListedForcesTest.Ifunc/18 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/19
7: [ OK ] Polarize/ListedForcesTest.Ifunc/19 (0 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/20
7: [ OK ] Polarize/ListedForcesTest.Ifunc/20 (0 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/21
7: [ OK ] Polarize/ListedForcesTest.Ifunc/21 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/22
7: [ OK ] Polarize/ListedForcesTest.Ifunc/22 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/23
7: [ OK ] Polarize/ListedForcesTest.Ifunc/23 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/24
7: [ OK ] Polarize/ListedForcesTest.Ifunc/24 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/25
7: [ OK ] Polarize/ListedForcesTest.Ifunc/25 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/26
7: [ OK ] Polarize/ListedForcesTest.Ifunc/26 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/27
7: [ OK ] Polarize/ListedForcesTest.Ifunc/27 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/28
7: [ OK ] Polarize/ListedForcesTest.Ifunc/28 (0 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/29
7: [ OK ] Polarize/ListedForcesTest.Ifunc/29 (0 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/30
7: [ OK ] Polarize/ListedForcesTest.Ifunc/30 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/31
7: [ OK ] Polarize/ListedForcesTest.Ifunc/31 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/32
7: [ OK ] Polarize/ListedForcesTest.Ifunc/32 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/33
7: [ OK ] Polarize/ListedForcesTest.Ifunc/33 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/34
7: [ OK ] Polarize/ListedForcesTest.Ifunc/34 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/35
7: [ OK ] Polarize/ListedForcesTest.Ifunc/35 (1 ms)
7: [----------] 36 tests from Polarize/ListedForcesTest (33 ms total)
7:
7: [----------] 54 tests from Restraints/ListedForcesTest
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/0
7: [ OK ] Restraints/ListedForcesTest.Ifunc/0 (2 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/1
7: [ OK ] Restraints/ListedForcesTest.Ifunc/1 (2 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/2
7: [ OK ] Restraints/ListedForcesTest.Ifunc/2 (2 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/3
7: [ OK ] Restraints/ListedForcesTest.Ifunc/3 (3 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/4
7: [ OK ] Restraints/ListedForcesTest.Ifunc/4 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/5
7: [ OK ] Restraints/ListedForcesTest.Ifunc/5 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/6
7: [ OK ] Restraints/ListedForcesTest.Ifunc/6 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/7
7: [ OK ] Restraints/ListedForcesTest.Ifunc/7 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/8
7: [ OK ] Restraints/ListedForcesTest.Ifunc/8 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/9
7: [ OK ] Restraints/ListedForcesTest.Ifunc/9 (0 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/10
7: [ OK ] Restraints/ListedForcesTest.Ifunc/10 (0 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/11
7: [ OK ] Restraints/ListedForcesTest.Ifunc/11 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/12
7: [ OK ] Restraints/ListedForcesTest.Ifunc/12 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/13
7: [ OK ] Restraints/ListedForcesTest.Ifunc/13 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/14
7: [ OK ] Restraints/ListedForcesTest.Ifunc/14 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/15
7: [ OK ] Restraints/ListedForcesTest.Ifunc/15 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/16
7: [ OK ] Restraints/ListedForcesTest.Ifunc/16 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/17
7: [ OK ] Restraints/ListedForcesTest.Ifunc/17 (0 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/18
7: [ OK ] Restraints/ListedForcesTest.Ifunc/18 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/19
7: [ OK ] Restraints/ListedForcesTest.Ifunc/19 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/20
7: [ OK ] Restraints/ListedForcesTest.Ifunc/20 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/21
7: [ OK ] Restraints/ListedForcesTest.Ifunc/21 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/22
7: [ OK ] Restraints/ListedForcesTest.Ifunc/22 (2 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/23
7: [ OK ] Restraints/ListedForcesTest.Ifunc/23 (2 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/24
7: [ OK ] Restraints/ListedForcesTest.Ifunc/24 (2 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/25
7: [ OK ] Restraints/ListedForcesTest.Ifunc/25 (2 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/26
7: [ OK ] Restraints/ListedForcesTest.Ifunc/26 (2 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/27
7: [ OK ] Restraints/ListedForcesTest.Ifunc/27 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/28
7: [ OK ] Restraints/ListedForcesTest.Ifunc/28 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/29
7: [ OK ] Restraints/ListedForcesTest.Ifunc/29 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/30
7: [ OK ] Restraints/ListedForcesTest.Ifunc/30 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/31
7: [ OK ] Restraints/ListedForcesTest.Ifunc/31 (0 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/32
7: [ OK ] Restraints/ListedForcesTest.Ifunc/32 (0 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/33
7: [ OK ] Restraints/ListedForcesTest.Ifunc/33 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/34
7: [ OK ] Restraints/ListedForcesTest.Ifunc/34 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/35
7: [ OK ] Restraints/ListedForcesTest.Ifunc/35 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/36
7: [ OK ] Restraints/ListedForcesTest.Ifunc/36 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/37
7: [ OK ] Restraints/ListedForcesTest.Ifunc/37 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/38
7: [ OK ] Restraints/ListedForcesTest.Ifunc/38 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/39
7: [ OK ] Restraints/ListedForcesTest.Ifunc/39 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/40
7: [ OK ] Restraints/ListedForcesTest.Ifunc/40 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/41
7: [ OK ] Restraints/ListedForcesTest.Ifunc/41 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/42
7: [ OK ] Restraints/ListedForcesTest.Ifunc/42 (0 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/43
7: [ OK ] Restraints/ListedForcesTest.Ifunc/43 (0 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/44
7: [ OK ] Restraints/ListedForcesTest.Ifunc/44 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/45
7: [ OK ] Restraints/ListedForcesTest.Ifunc/45 (2 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/46
7: [ OK ] Restraints/ListedForcesTest.Ifunc/46 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/47
7: [ OK ] Restraints/ListedForcesTest.Ifunc/47 (2 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/48
7: [ OK ] Restraints/ListedForcesTest.Ifunc/48 (2 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/49
7: [ OK ] Restraints/ListedForcesTest.Ifunc/49 (2 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/50
7: [ OK ] Restraints/ListedForcesTest.Ifunc/50 (2 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/51
7: [ OK ] Restraints/ListedForcesTest.Ifunc/51 (2 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/52
7: [ OK ] Restraints/ListedForcesTest.Ifunc/52 (2 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/53
7: [ OK ] Restraints/ListedForcesTest.Ifunc/53 (2 ms)
7: [----------] 54 tests from Restraints/ListedForcesTest (79 ms total)
7:
7: [----------] Global test environment tear-down
7: [==========] 315 tests from 5 test cases ran. (592 ms total)
7: [ PASSED ] 315 tests.
7/52 Test #7: ListedForcesTest .................... Passed 0.79 sec
test 8
Start 8: CommandLineUnitTests
8: Test command: /<<PKGBUILDDIR>>/build/basic/bin/commandline-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/CommandLineUnitTests.xml"
8: Test timeout computed to be: 30
8: [==========] Running 59 tests from 7 test cases.
8: [----------] Global test environment set-up.
8: [----------] 3 tests from CommandLineHelpModuleTest
8: [ RUN ] CommandLineHelpModuleTest.PrintsGeneralHelp
8: [ OK ] CommandLineHelpModuleTest.PrintsGeneralHelp (5 ms)
8: [ RUN ] CommandLineHelpModuleTest.PrintsHelpOnTopic
8: [ OK ] CommandLineHelpModuleTest.PrintsHelpOnTopic (2 ms)
8: [ RUN ] CommandLineHelpModuleTest.ExportsHelp
8: [ OK ] CommandLineHelpModuleTest.ExportsHelp (11 ms)
8: [----------] 3 tests from CommandLineHelpModuleTest (20 ms total)
8:
8: [----------] 7 tests from CommandLineHelpWriterTest
8: [ RUN ] CommandLineHelpWriterTest.HandlesOptionTypes
8: [ OK ] CommandLineHelpWriterTest.HandlesOptionTypes (3 ms)
8: [ RUN ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables
8: [ OK ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables (1 ms)
8: [ RUN ] CommandLineHelpWriterTest.HandlesLongFileOptions
8: [ OK ] CommandLineHelpWriterTest.HandlesLongFileOptions (1 ms)
8: [ RUN ] CommandLineHelpWriterTest.HandlesLongOptions
8: [ OK ] CommandLineHelpWriterTest.HandlesLongOptions (1 ms)
8: [ RUN ] CommandLineHelpWriterTest.HandlesOptionGroups
8: [ OK ] CommandLineHelpWriterTest.HandlesOptionGroups (1 ms)
8: [ RUN ] CommandLineHelpWriterTest.HandlesHelpText
8: [ OK ] CommandLineHelpWriterTest.HandlesHelpText (1 ms)
8: [ RUN ] CommandLineHelpWriterTest.HandlesKnownIssues
8: [ OK ] CommandLineHelpWriterTest.HandlesKnownIssues (1 ms)
8: [----------] 7 tests from CommandLineHelpWriterTest (13 ms total)
8:
8: [----------] 6 tests from CommandLineModuleManagerTest
8: [ RUN ] CommandLineModuleManagerTest.RunsModule
8: [ OK ] CommandLineModuleManagerTest.RunsModule (1 ms)
8: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelp
8: [ OK ] CommandLineModuleManagerTest.RunsModuleHelp (1 ms)
8: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet
8: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet (1 ms)
8: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH
8: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH (1 ms)
8: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule
8: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule (0 ms)
8: [ RUN ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames
8: [ OK ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames (0 ms)
8: [----------] 6 tests from CommandLineModuleManagerTest (6 ms total)
8:
8: [----------] 13 tests from CommandLineParserTest
8: [ RUN ] CommandLineParserTest.HandlesSingleValues
8: [ OK ] CommandLineParserTest.HandlesSingleValues (0 ms)
8: [ RUN ] CommandLineParserTest.HandlesBooleanWithoutArgument
8: [ OK ] CommandLineParserTest.HandlesBooleanWithoutArgument (0 ms)
8: [ RUN ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument
8: [ OK ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument (0 ms)
8: [ RUN ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument
8: [ OK ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument (1 ms)
8: [ RUN ] CommandLineParserTest.HandlesNegativeNumbers
8: [ OK ] CommandLineParserTest.HandlesNegativeNumbers (0 ms)
8: [ RUN ] CommandLineParserTest.HandlesString
8: [ OK ] CommandLineParserTest.HandlesString (0 ms)
8: [ RUN ] CommandLineParserTest.RejectsStringWithMultipleValues
8: [ OK ] CommandLineParserTest.RejectsStringWithMultipleValues (0 ms)
8: [ RUN ] CommandLineParserTest.HandlesDoubleDashOptionPrefix
8: [ OK ] CommandLineParserTest.HandlesDoubleDashOptionPrefix (0 ms)
8: [ RUN ] CommandLineParserTest.HandlesOptionsStartingWithNumbers
8: [ OK ] CommandLineParserTest.HandlesOptionsStartingWithNumbers (0 ms)
8: [ RUN ] CommandLineParserTest.HandlesSkipUnknown
8: [ OK ] CommandLineParserTest.HandlesSkipUnknown (0 ms)
8: [ RUN ] CommandLineParserTest.RejectsPositionalArgumentsByDefault
8: [ OK ] CommandLineParserTest.RejectsPositionalArgumentsByDefault (0 ms)
8: [ RUN ] CommandLineParserTest.CanAllowPositionalArguments
8: [ OK ] CommandLineParserTest.CanAllowPositionalArguments (0 ms)
8: [ RUN ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions
8: [ OK ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions (0 ms)
8: [----------] 13 tests from CommandLineParserTest (8 ms total)
8:
8: [----------] 6 tests from CommandLineProgramContextTest
8: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath
8: [ OK ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath (0 ms)
8: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithRelativePath
8: [ OK ] CommandLineProgramContextTest.FindsBinaryWithRelativePath (0 ms)
8: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromPath
8: [ OK ] CommandLineProgramContextTest.FindsBinaryFromPath (0 ms)
8: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory
8: [ OK ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory (0 ms)
8: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink
8: [ OK ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink (0 ms)
8: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink
8: [ OK ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink (0 ms)
8: [----------] 6 tests from CommandLineProgramContextTest (3 ms total)
8:
8: [----------] 3 tests from OutputNamesTest
8: [ RUN ] OutputNamesTest.CanBeSuffixed
8: [ OK ] OutputNamesTest.CanBeSuffixed (0 ms)
8: [ RUN ] OutputNamesTest.HasSuffixFromNoAppend
8: [ OK ] OutputNamesTest.HasSuffixFromNoAppend (0 ms)
8: [ RUN ] OutputNamesTest.CanHavePartNumberAdded
8: [ OK ] OutputNamesTest.CanHavePartNumberAdded (0 ms)
8: [----------] 3 tests from OutputNamesTest (1 ms total)
8:
8: [----------] 21 tests from ParseCommonArgsTest
8: [ RUN ] ParseCommonArgsTest.ParsesIntegerArgs
8: [ OK ] ParseCommonArgsTest.ParsesIntegerArgs (0 ms)
8: [ RUN ] ParseCommonArgsTest.ParsesInt64Args
8: [ OK ] ParseCommonArgsTest.ParsesInt64Args (0 ms)
8: [ RUN ] ParseCommonArgsTest.ParsesRealArgs
8: [ OK ] ParseCommonArgsTest.ParsesRealArgs (1 ms)
8: [ RUN ] ParseCommonArgsTest.ParsesStringArgs
8: [ OK ] ParseCommonArgsTest.ParsesStringArgs (0 ms)
8: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgs
8: [ OK ] ParseCommonArgsTest.ParsesBooleanArgs (0 ms)
8: [ RUN ] ParseCommonArgsTest.ParsesVectorArgs
8: [ OK ] ParseCommonArgsTest.ParsesVectorArgs (0 ms)
8: [ RUN ] ParseCommonArgsTest.ParsesTimeArgs
8: [ OK ] ParseCommonArgsTest.ParsesTimeArgs (0 ms)
8: [ RUN ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit
8: [ OK ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit (1 ms)
8: [ RUN ] ParseCommonArgsTest.ParsesEnumArgs
8: [ OK ] ParseCommonArgsTest.ParsesEnumArgs (0 ms)
8: [ RUN ] ParseCommonArgsTest.ParsesFileArgs
8: [ OK ] ParseCommonArgsTest.ParsesFileArgs (0 ms)
8: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaults
8: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaults (1 ms)
8: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName
8: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName (0 ms)
8: [ RUN ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension
8: [ OK ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension (0 ms)
8: [ RUN ] ParseCommonArgsTest.HandlesNonExistentInputFiles
8: [ OK ] ParseCommonArgsTest.HandlesNonExistentInputFiles (1 ms)
8: [ RUN ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles
8: [ OK ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles (1 ms)
8: [ RUN ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified
8: [ OK ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified (1 ms)
8: [ RUN ] ParseCommonArgsTest.HandlesCompressedFiles
8: [ OK ] ParseCommonArgsTest.HandlesCompressedFiles (2 ms)
8: [ RUN ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension
8: [ OK ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension (1 ms)
8: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFile
8: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFile (4 ms)
8: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName
8: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName (3 ms)
8: [ RUN ] ParseCommonArgsTest.CanKeepUnknownArgs
8: [ OK ] ParseCommonArgsTest.CanKeepUnknownArgs (0 ms)
8: [----------] 21 tests from ParseCommonArgsTest (23 ms total)
8:
8: [----------] Global test environment tear-down
8: [==========] 59 tests from 7 test cases ran. (81 ms total)
8: [ PASSED ] 59 tests.
8/52 Test #8: CommandLineUnitTests ................ Passed 0.15 sec
test 9
Start 9: DomDecTests
9: Test command: /<<PKGBUILDDIR>>/build/basic/bin/domdec-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/DomDecTests.xml"
9: Test timeout computed to be: 30
9: [==========] Running 9 tests from 2 test cases.
9: [----------] Global test environment set-up.
9: [----------] 7 tests from HashedMap
9: [ RUN ] HashedMap.InsertsFinds
9: [ OK ] HashedMap.InsertsFinds (0 ms)
9: [ RUN ] HashedMap.NegativeKeysWork
9: [ OK ] HashedMap.NegativeKeysWork (0 ms)
9: [ RUN ] HashedMap.InsertsErases
9: [ OK ] HashedMap.InsertsErases (0 ms)
9: [ RUN ] HashedMap.InsertsOrAssigns
9: [ OK ] HashedMap.InsertsOrAssigns (0 ms)
9: [ RUN ] HashedMap.Clears
9: [ OK ] HashedMap.Clears (0 ms)
9: [ RUN ] HashedMap.LinkedEntries
9: [ OK ] HashedMap.LinkedEntries (0 ms)
9: [ RUN ] HashedMap.ResizesTable
9: [ OK ] HashedMap.ResizesTable (0 ms)
9: [----------] 7 tests from HashedMap (1 ms total)
9:
9: [----------] 2 tests from LocalAtomSetManager
9: [ RUN ] LocalAtomSetManager.CanAddEmptyLocalAtomSet
9: [ OK ] LocalAtomSetManager.CanAddEmptyLocalAtomSet (0 ms)
9: [ RUN ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices
9: [ OK ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices (0 ms)
9: [----------] 2 tests from LocalAtomSetManager (0 ms total)
9:
9: [----------] Global test environment tear-down
9: [==========] 9 tests from 2 test cases ran. (1 ms total)
9: [ PASSED ] 9 tests.
9/52 Test #9: DomDecTests ......................... Passed 0.06 sec
test 10
Start 10: EwaldUnitTests
10: Test command: /<<PKGBUILDDIR>>/build/basic/bin/ewald-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/EwaldUnitTests.xml"
10: Test timeout computed to be: 30
10: [==========] Running 257 tests from 10 test cases.
10: [----------] Global test environment set-up.
10: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest
10: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0
10: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 (1 ms)
10: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1
10: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 (1 ms)
10: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2
10: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 (1 ms)
10: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3
10: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 (13 ms)
10: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4
10: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 (1 ms)
10: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest (17 ms total)
10:
10: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 (40 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 (9 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 (21 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 (9 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 (13 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 (9 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 (18 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 (9 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 (27 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 (10 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 (10 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 (9 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 (34 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 (11 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 (11 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 (11 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 (11 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 (11 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 (11 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 (11 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 (11 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 (11 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 (12 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 (12 ms)
10: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest (356 ms total)
10:
10: [----------] 144 tests from SaneInput/PmeGatherTest
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/0
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/0 (8 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/1
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/1 (21 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/2
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/2 (6 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/3
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/3 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/4
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/4 (3 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/5
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/5 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/6
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/6 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/7
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/7 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/8
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/8 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/9
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/9 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/10
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/10 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/11
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/11 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/12
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/12 (3 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/13
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/13 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/14
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/14 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/15
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/15 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/16
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/16 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/17
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/17 (9 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/18
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/18 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/19
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/19 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/20
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/20 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/21
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/21 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/22
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/22 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/23
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/23 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/24
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/24 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/25
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/25 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/26
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/26 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/27
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/27 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/28
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/28 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/29
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/29 (3 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/30
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/30 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/31
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/31 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/32
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/32 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/33
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/33 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/34
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/34 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/35
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/35 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/36
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/36 (10 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/37
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/37 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/38
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/38 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/39
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/39 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/40
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/40 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/41
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/41 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/42
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/42 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/43
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/43 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/44
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/44 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/45
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/45 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/46
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/46 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/47
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/47 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/48
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/48 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/49
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/49 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/50
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/50 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/51
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/51 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/52
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/52 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/53
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/53 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/54
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/54 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/55
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/55 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/56
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/56 (3 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/57
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/57 (3 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/58
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/58 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/59
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/59 (3 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/60
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/60 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/61
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/61 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/62
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/62 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/63
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/63 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/64
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/64 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/65
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/65 (3 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/66
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/66 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/67
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/67 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/68
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/68 (3 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/69
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/69 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/70
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/70 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/71
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/71 (18 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/72
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/72 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/73
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/73 (4 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/74
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/74 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/75
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/75 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/76
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/76 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/77
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/77 (10 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/78
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/78 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/79
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/79 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/80
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/80 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/81
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/81 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/82
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/82 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/83
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/83 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/84
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/84 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/85
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/85 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/86
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/86 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/87
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/87 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/88
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/88 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/89
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/89 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/90
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/90 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/91
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/91 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/92
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/92 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/93
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/93 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/94
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/94 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/95
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/95 (3 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/96
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/96 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/97
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/97 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/98
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/98 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/99
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/99 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/100
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/100 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/101
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/101 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/102
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/102 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/103
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/103 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/104
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/104 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/105
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/105 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/106
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/106 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/107
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/107 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/108
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/108 (5 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/109
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/109 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/110
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/110 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/111
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/111 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/112
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/112 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/113
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/113 (3 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/114
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/114 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/115
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/115 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/116
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/116 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/117
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/117 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/118
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/118 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/119
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/119 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/120
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/120 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/121
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/121 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/122
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/122 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/123
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/123 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/124
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/124 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/125
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/125 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/126
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/126 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/127
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/127 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/128
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/128 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/129
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/129 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/130
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/130 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/131
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/131 (3 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/132
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/132 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/133
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/133 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/134
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/134 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/135
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/135 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/136
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/136 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/137
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/137 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/138
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/138 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/139
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/139 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/140
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/140 (4 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/141
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/141 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/142
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/142 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/143
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/143 (3 ms)
10: [----------] 144 tests from SaneInput/PmeGatherTest (373 ms total)
10:
10: [----------] 16 tests from SaneInput/PmeSolveTest
10: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/0
10: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/0 (8 ms)
10: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/1
10: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/1 (9 ms)
10: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/2
10: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/2 (5 ms)
10: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/3
10: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/3 (8 ms)
10: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/4
10: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/4 (10 ms)
10: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/5
10: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/5 (6 ms)
10: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/6
10: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/6 (4 ms)
10: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/7
10: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/7 (5 ms)
10: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/8
10: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/8 (6 ms)
10: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/9
10: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/9 (9 ms)
10: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/10
10: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/10 (5 ms)
10: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/11
10: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/11 (9 ms)
10: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/12
10: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/12 (4 ms)
10: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/13
10: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/13 (6 ms)
10: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/14
10: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/14 (3 ms)
10: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/15
10: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/15 (5 ms)
10: [----------] 16 tests from SaneInput/PmeSolveTest (103 ms total)
10:
10: [----------] 8 tests from DifferentEwaldCoeffQ/PmeSolveTest
10: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/0
10: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/0 (5 ms)
10: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/1
10: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/1 (5 ms)
10: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/2
10: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/2 (3 ms)
10: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/3
10: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/3 (4 ms)
10: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/4
10: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/4 (5 ms)
10: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/5
10: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/5 (5 ms)
10: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/6
10: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/6 (3 ms)
10: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/7
10: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/7 (4 ms)
10: [----------] 8 tests from DifferentEwaldCoeffQ/PmeSolveTest (34 ms total)
10:
10: [----------] 8 tests from DifferentEwaldCoeffLJ/PmeSolveTest
10: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/0
10: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/0 (9 ms)
10: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/1
10: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/1 (9 ms)
10: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/2
10: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/2 (6 ms)
10: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/3
10: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/3 (6 ms)
10: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/4
10: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/4 (9 ms)
10: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/5
10: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/5 (9 ms)
10: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/6
10: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/6 (6 ms)
10: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/7
10: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/7 (5 ms)
10: [----------] 8 tests from DifferentEwaldCoeffLJ/PmeSolveTest (59 ms total)
10:
10: [----------] 16 tests from DifferentEpsilonR/PmeSolveTest
10: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/0
10: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/0 (5 ms)
10: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/1
10: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/1 (9 ms)
10: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/2
10: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/2 (5 ms)
10: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/3
10: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/3 (9 ms)
10: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/4
10: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/4 (3 ms)
10: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/5
10: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/5 (6 ms)
10: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/6
10: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/6 (3 ms)
10: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/7
10: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/7 (5 ms)
10: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/8
10: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/8 (5 ms)
10: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/9
10: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/9 (9 ms)
10: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/10
10: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/10 (5 ms)
10: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/11
10: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/11 (9 ms)
10: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/12
10: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/12 (4 ms)
10: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/13
10: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/13 (6 ms)
10: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/14
10: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/14 (3 ms)
10: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/15
10: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/15 (6 ms)
10: [----------] 16 tests from DifferentEpsilonR/PmeSolveTest (93 ms total)
10:
10: [----------] 12 tests from SaneInput1/PmeSplineAndSpreadTest
10: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/0
10: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/0 (5 ms)
10: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/1
10: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/1 (14 ms)
10: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/2
10: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/2 (7 ms)
10: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/3
10: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/3 (7 ms)
10: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/4
10: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/4 (8 ms)
10: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/5
10: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/5 (9 ms)
10: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/6
10: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/6 (5 ms)
10: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/7
10: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/7 (6 ms)
10: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/8
10: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/8 (6 ms)
10: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/9
10: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/9 (8 ms)
10: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/10
10: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/10 (9 ms)
10: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/11
10: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/11 (10 ms)
10: [----------] 12 tests from SaneInput1/PmeSplineAndSpreadTest (99 ms total)
10:
10: [----------] 12 tests from SaneInput2/PmeSplineAndSpreadTest
10: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/0
10: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/0 (6 ms)
10: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/1
10: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/1 (7 ms)
10: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/2
10: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/2 (8 ms)
10: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/3
10: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/3 (9 ms)
10: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/4
10: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/4 (10 ms)
10: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/5
10: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/5 (12 ms)
10: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/6
10: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/6 (7 ms)
10: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/7
10: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/7 (7 ms)
10: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/8
10: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/8 (9 ms)
10: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/9
10: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/9 (9 ms)
10: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/10
10: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/10 (13 ms)
10: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/11
10: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/11 (14 ms)
10: [----------] 12 tests from SaneInput2/PmeSplineAndSpreadTest (119 ms total)
10:
10: [----------] 12 tests from SaneInput13/PmeSplineAndSpreadTest
10: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/0
10: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/0 (16 ms)
10: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/1
10: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/1 (18 ms)
10: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/2
10: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/2 (24 ms)
10: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/3
10: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/3 (27 ms)
10: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/4
10: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/4 (46 ms)
10: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/5
10: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/5 (39 ms)
10: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/6
10: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/6 (17 ms)
10: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/7
10: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/7 (18 ms)
10: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/8
10: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/8 (24 ms)
10: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/9
10: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/9 (26 ms)
10: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/10
10: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/10 (33 ms)
10: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/11
10: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/11 (37 ms)
10: [----------] 12 tests from SaneInput13/PmeSplineAndSpreadTest (350 ms total)
10:
10: [----------] Global test environment tear-down
10: [==========] 257 tests from 10 test cases ran. (2052 ms total)
10: [ PASSED ] 257 tests.
10/52 Test #10: EwaldUnitTests ...................... Passed 2.26 sec
test 11
Start 11: FFTUnitTests
11: Test command: /<<PKGBUILDDIR>>/build/basic/bin/fft-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/FFTUnitTests.xml"
11: Test timeout computed to be: 30
11: [==========] Running 14 tests from 4 test cases.
11: [----------] Global test environment set-up.
11: [----------] 2 tests from ManyFFTTest
11: [ RUN ] ManyFFTTest.Complex1DLength48Multi5Test
11: [ OK ] ManyFFTTest.Complex1DLength48Multi5Test (61 ms)
11: [ RUN ] ManyFFTTest.Real1DLength48Multi5Test
11: [ OK ] ManyFFTTest.Real1DLength48Multi5Test (62 ms)
11: [----------] 2 tests from ManyFFTTest (127 ms total)
11:
11: [----------] 1 test from FFTTest
11: [ RUN ] FFTTest.Real2DLength18_15Test
11: [ OK ] FFTTest.Real2DLength18_15Test (20 ms)
11: [----------] 1 test from FFTTest (22 ms total)
11:
11: [----------] 1 test from FFFTest3D
11: [ RUN ] FFFTest3D.Real5_6_9
11: [ OK ] FFFTest3D.Real5_6_9 (12 ms)
11: [----------] 1 test from FFFTest3D (13 ms total)
11:
11: [----------] 10 tests from 7_8_25_36_60/FFTTest1D
11: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/0
11: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/0 (3 ms)
11: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/1
11: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/1 (3 ms)
11: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/2
11: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/2 (16 ms)
11: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/3
11: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/3 (12 ms)
11: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/4
11: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/4 (9 ms)
11: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/0
11: [ OK ] 7_8_25_36_60/FFTTest1D.Real/0 (3 ms)
11: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/1
11: [ OK ] 7_8_25_36_60/FFTTest1D.Real/1 (3 ms)
11: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/2
11: [ OK ] 7_8_25_36_60/FFTTest1D.Real/2 (3 ms)
11: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/3
11: [ OK ] 7_8_25_36_60/FFTTest1D.Real/3 (30 ms)
11: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/4
11: [ OK ] 7_8_25_36_60/FFTTest1D.Real/4 (43 ms)
11: [----------] 10 tests from 7_8_25_36_60/FFTTest1D (130 ms total)
11:
11: [----------] Global test environment tear-down
11: [==========] 14 tests from 4 test cases ran. (294 ms total)
11: [ PASSED ] 14 tests.
11/52 Test #11: FFTUnitTests ........................ Passed 0.36 sec
test 12
Start 12: GpuUtilsUnitTests
12: Test command: /<<PKGBUILDDIR>>/build/basic/bin/gpu_utils-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/GpuUtilsUnitTests.xml"
12: Test timeout computed to be: 30
12: [==========] Running 62 tests from 20 test cases.
12: [----------] Global test environment set-up.
12: [----------] 2 tests from ClfftInitializer
12: [ RUN ] ClfftInitializer.SingleInitializationWorks
12: [ OK ] ClfftInitializer.SingleInitializationWorks (0 ms)
12: [ RUN ] ClfftInitializer.TwoInitializationsWork
12: [ OK ] ClfftInitializer.TwoInitializationsWork (0 ms)
12: [----------] 2 tests from ClfftInitializer (0 ms total)
12:
12: [----------] 2 tests from HostAllocatorTest/0, where TypeParam = int
12: [ RUN ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks
12: [ OK ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks (0 ms)
12: [ RUN ] HostAllocatorTest/0.StatefulAllocatorUsesMemory
12: [ OK ] HostAllocatorTest/0.StatefulAllocatorUsesMemory (0 ms)
12: [----------] 2 tests from HostAllocatorTest/0 (0 ms total)
12:
12: [----------] 2 tests from HostAllocatorTest/1, where TypeParam = float
12: [ RUN ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks
12: [ OK ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks (0 ms)
12: [ RUN ] HostAllocatorTest/1.StatefulAllocatorUsesMemory
12: [ OK ] HostAllocatorTest/1.StatefulAllocatorUsesMemory (0 ms)
12: [----------] 2 tests from HostAllocatorTest/1 (0 ms total)
12:
12: [----------] 2 tests from HostAllocatorTest/2, where TypeParam = gmx::BasicVector<float>
12: [ RUN ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks
12: [ OK ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks (0 ms)
12: [ RUN ] HostAllocatorTest/2.StatefulAllocatorUsesMemory
12: [ OK ] HostAllocatorTest/2.StatefulAllocatorUsesMemory (0 ms)
12: [----------] 2 tests from HostAllocatorTest/2 (0 ms total)
12:
12: [----------] 2 tests from HostAllocatorTest/3, where TypeParam = gmx::test::MoveOnly
12: [ RUN ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks
12: [ OK ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks (0 ms)
12: [ RUN ] HostAllocatorTest/3.StatefulAllocatorUsesMemory
12: [ OK ] HostAllocatorTest/3.StatefulAllocatorUsesMemory (0 ms)
12: [----------] 2 tests from HostAllocatorTest/3 (0 ms total)
12:
12: [----------] 3 tests from HostAllocatorTestCopyable/0, where TypeParam = int
12: [ RUN ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks
12: [ OK ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms)
12: [ RUN ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork
12: [ OK ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork (0 ms)
12: [ RUN ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve
12: [ OK ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve (0 ms)
12: [----------] 3 tests from HostAllocatorTestCopyable/0 (0 ms total)
12:
12: [----------] 3 tests from HostAllocatorTestCopyable/1, where TypeParam = float
12: [ RUN ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks
12: [ OK ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms)
12: [ RUN ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork
12: [ OK ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork (0 ms)
12: [ RUN ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve
12: [ OK ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve (0 ms)
12: [----------] 3 tests from HostAllocatorTestCopyable/1 (0 ms total)
12:
12: [----------] 3 tests from HostAllocatorTestCopyable/2, where TypeParam = gmx::BasicVector<float>
12: [ RUN ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks
12: [ OK ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms)
12: [ RUN ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork
12: [ OK ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork (0 ms)
12: [ RUN ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve
12: [ OK ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve (0 ms)
12: [----------] 3 tests from HostAllocatorTestCopyable/2 (0 ms total)
12:
12: [----------] 5 tests from HostAllocatorTestNoMem/0, where TypeParam = int
12: [ RUN ] HostAllocatorTestNoMem/0.CreateVector
12: [ OK ] HostAllocatorTestNoMem/0.CreateVector (0 ms)
12: [ RUN ] HostAllocatorTestNoMem/0.MoveAssignment
12: [ OK ] HostAllocatorTestNoMem/0.MoveAssignment (0 ms)
12: [ RUN ] HostAllocatorTestNoMem/0.MoveConstruction
12: [ OK ] HostAllocatorTestNoMem/0.MoveConstruction (0 ms)
12: [ RUN ] HostAllocatorTestNoMem/0.Swap
12: [ OK ] HostAllocatorTestNoMem/0.Swap (0 ms)
12: [ RUN ] HostAllocatorTestNoMem/0.Comparison
12: [ OK ] HostAllocatorTestNoMem/0.Comparison (0 ms)
12: [----------] 5 tests from HostAllocatorTestNoMem/0 (1 ms total)
12:
12: [----------] 5 tests from HostAllocatorTestNoMem/1, where TypeParam = float
12: [ RUN ] HostAllocatorTestNoMem/1.CreateVector
12: [ OK ] HostAllocatorTestNoMem/1.CreateVector (0 ms)
12: [ RUN ] HostAllocatorTestNoMem/1.MoveAssignment
12: [ OK ] HostAllocatorTestNoMem/1.MoveAssignment (0 ms)
12: [ RUN ] HostAllocatorTestNoMem/1.MoveConstruction
12: [ OK ] HostAllocatorTestNoMem/1.MoveConstruction (0 ms)
12: [ RUN ] HostAllocatorTestNoMem/1.Swap
12: [ OK ] HostAllocatorTestNoMem/1.Swap (0 ms)
12: [ RUN ] HostAllocatorTestNoMem/1.Comparison
12: [ OK ] HostAllocatorTestNoMem/1.Comparison (0 ms)
12: [----------] 5 tests from HostAllocatorTestNoMem/1 (0 ms total)
12:
12: [----------] 5 tests from HostAllocatorTestNoMem/2, where TypeParam = gmx::BasicVector<float>
12: [ RUN ] HostAllocatorTestNoMem/2.CreateVector
12: [ OK ] HostAllocatorTestNoMem/2.CreateVector (0 ms)
12: [ RUN ] HostAllocatorTestNoMem/2.MoveAssignment
12: [ OK ] HostAllocatorTestNoMem/2.MoveAssignment (0 ms)
12: [ RUN ] HostAllocatorTestNoMem/2.MoveConstruction
12: [ OK ] HostAllocatorTestNoMem/2.MoveConstruction (0 ms)
12: [ RUN ] HostAllocatorTestNoMem/2.Swap
12: [ OK ] HostAllocatorTestNoMem/2.Swap (0 ms)
12: [ RUN ] HostAllocatorTestNoMem/2.Comparison
12: [ OK ] HostAllocatorTestNoMem/2.Comparison (0 ms)
12: [----------] 5 tests from HostAllocatorTestNoMem/2 (0 ms total)
12:
12: [----------] 5 tests from HostAllocatorTestNoMem/3, where TypeParam = gmx::test::MoveOnly
12: [ RUN ] HostAllocatorTestNoMem/3.CreateVector
12: [ OK ] HostAllocatorTestNoMem/3.CreateVector (0 ms)
12: [ RUN ] HostAllocatorTestNoMem/3.MoveAssignment
12: [ OK ] HostAllocatorTestNoMem/3.MoveAssignment (0 ms)
12: [ RUN ] HostAllocatorTestNoMem/3.MoveConstruction
12: [ OK ] HostAllocatorTestNoMem/3.MoveConstruction (0 ms)
12: [ RUN ] HostAllocatorTestNoMem/3.Swap
12: [ OK ] HostAllocatorTestNoMem/3.Swap (0 ms)
12: [ RUN ] HostAllocatorTestNoMem/3.Comparison
12: [ OK ] HostAllocatorTestNoMem/3.Comparison (0 ms)
12: [----------] 5 tests from HostAllocatorTestNoMem/3 (1 ms total)
12:
12: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0, where TypeParam = int
12: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyAssignment
12: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyAssignment (0 ms)
12: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstruction
12: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstruction (0 ms)
12: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0 (0 ms total)
12:
12: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1, where TypeParam = float
12: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyAssignment
12: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyAssignment (0 ms)
12: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstruction
12: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstruction (0 ms)
12: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1 (0 ms total)
12:
12: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2, where TypeParam = gmx::BasicVector<float>
12: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyAssignment
12: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyAssignment (0 ms)
12: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstruction
12: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstruction (0 ms)
12: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2 (0 ms total)
12:
12: [----------] 1 test from HostAllocatorUntypedTest
12: [ RUN ] HostAllocatorUntypedTest.Comparison
12: [ OK ] HostAllocatorUntypedTest.Comparison (0 ms)
12: [----------] 1 test from HostAllocatorUntypedTest (0 ms total)
12:
12: [----------] 4 tests from AllocatorTest/0, where TypeParam = gmx::Allocator<float, gmx::HostAllocationPolicy>
12: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment
12: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms)
12: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment
12: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (1 ms)
12: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment
12: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms)
12: [ RUN ] AllocatorTest/0.Move
12: [ OK ] AllocatorTest/0.Move (0 ms)
12: [----------] 4 tests from AllocatorTest/0 (1 ms total)
12:
12: [----------] 4 tests from AllocatorTest/1, where TypeParam = gmx::Allocator<int, gmx::HostAllocationPolicy>
12: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment
12: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms)
12: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment
12: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (1 ms)
12: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment
12: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms)
12: [ RUN ] AllocatorTest/1.Move
12: [ OK ] AllocatorTest/1.Move (0 ms)
12: [----------] 4 tests from AllocatorTest/1 (1 ms total)
12:
12: [----------] 4 tests from AllocatorTest/2, where TypeParam = gmx::Allocator<gmx::BasicVector<float>, gmx::HostAllocationPolicy>
12: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment
12: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms)
12: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment
12: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (1 ms)
12: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment
12: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms)
12: [ RUN ] AllocatorTest/2.Move
12: [ OK ] AllocatorTest/2.Move (0 ms)
12: [----------] 4 tests from AllocatorTest/2 (1 ms total)
12:
12: [----------] 4 tests from AllocatorTest/3, where TypeParam = gmx::Allocator<gmx::test::MoveOnly, gmx::HostAllocationPolicy>
12: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment
12: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms)
12: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment
12: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (1 ms)
12: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment
12: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms)
12: [ RUN ] AllocatorTest/3.Move
12: [ OK ] AllocatorTest/3.Move (0 ms)
12: [----------] 4 tests from AllocatorTest/3 (1 ms total)
12:
12: [----------] Global test environment tear-down
12: [==========] 62 tests from 20 test cases ran. (8 ms total)
12: [ PASSED ] 62 tests.
12/52 Test #12: GpuUtilsUnitTests ................... Passed 0.08 sec
test 13
Start 13: HardwareUnitTests
13: Test command: /<<PKGBUILDDIR>>/build/basic/bin/hardware-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/HardwareUnitTests.xml"
13: Test timeout computed to be: 30
13: [==========] Running 4 tests from 1 test case.
13: [----------] Global test environment set-up.
13: [----------] 4 tests from HardwareTopologyTest
13: [ RUN ] HardwareTopologyTest.Execute
13: [ OK ] HardwareTopologyTest.Execute (33 ms)
13: [ RUN ] HardwareTopologyTest.HwlocExecute
13: [ OK ] HardwareTopologyTest.HwlocExecute (31 ms)
13: [ RUN ] HardwareTopologyTest.ProcessorSelfconsistency
13: [ OK ] HardwareTopologyTest.ProcessorSelfconsistency (32 ms)
13: [ RUN ] HardwareTopologyTest.NumaCacheSelfconsistency
13: [ OK ] HardwareTopologyTest.NumaCacheSelfconsistency (31 ms)
13: [----------] 4 tests from HardwareTopologyTest (128 ms total)
13:
13: [----------] Global test environment tear-down
13: [==========] 4 tests from 1 test case ran. (129 ms total)
13: [ PASSED ] 4 tests.
13/52 Test #13: HardwareUnitTests ................... Passed 0.19 sec
test 14
Start 14: MathUnitTests
14: Test command: /<<PKGBUILDDIR>>/build/basic/bin/math-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MathUnitTests.xml"
14: Test timeout computed to be: 30
14: [==========] Running 204 tests from 29 test cases.
14: [----------] Global test environment set-up.
14: [----------] 1 test from EmptyArrayRefWithPaddingTest
14: [ RUN ] EmptyArrayRefWithPaddingTest.IsEmpty
14: [ OK ] EmptyArrayRefWithPaddingTest.IsEmpty (0 ms)
14: [----------] 1 test from EmptyArrayRefWithPaddingTest (0 ms total)
14:
14: [----------] 1 test from EmptyConstArrayRefWithPaddingTest
14: [ RUN ] EmptyConstArrayRefWithPaddingTest.IsEmpty
14: [ OK ] EmptyConstArrayRefWithPaddingTest.IsEmpty (0 ms)
14: [----------] 1 test from EmptyConstArrayRefWithPaddingTest (0 ms total)
14:
14: [----------] 2 tests from ArrayRefWithPaddingTest/0, where TypeParam = gmx::ArrayRefWithPadding<int>
14: [ RUN ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks
14: [ OK ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks (0 ms)
14: [ RUN ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks
14: [ OK ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks (0 ms)
14: [----------] 2 tests from ArrayRefWithPaddingTest/0 (0 ms total)
14:
14: [----------] 2 tests from ArrayRefWithPaddingTest/1, where TypeParam = gmx::ArrayRefWithPadding<float>
14: [ RUN ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks
14: [ OK ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks (0 ms)
14: [ RUN ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks
14: [ OK ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks (0 ms)
14: [----------] 2 tests from ArrayRefWithPaddingTest/1 (0 ms total)
14:
14: [----------] 2 tests from ArrayRefWithPaddingTest/2, where TypeParam = gmx::ArrayRefWithPadding<double>
14: [ RUN ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks
14: [ OK ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks (0 ms)
14: [ RUN ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks
14: [ OK ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks (0 ms)
14: [----------] 2 tests from ArrayRefWithPaddingTest/2 (0 ms total)
14:
14: [----------] 8 tests from TranslateAndScaleTest
14: [ RUN ] TranslateAndScaleTest.identityTransformation
14: [ OK ] TranslateAndScaleTest.identityTransformation (1 ms)
14: [ RUN ] TranslateAndScaleTest.translationWithIdentityScaling
14: [ OK ] TranslateAndScaleTest.translationWithIdentityScaling (0 ms)
14: [ RUN ] TranslateAndScaleTest.scalingWithZeroTranslation
14: [ OK ] TranslateAndScaleTest.scalingWithZeroTranslation (0 ms)
14: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivial
14: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivial (0 ms)
14: [ RUN ] TranslateAndScaleTest.scalingIdentity
14: [ OK ] TranslateAndScaleTest.scalingIdentity (1 ms)
14: [ RUN ] TranslateAndScaleTest.scalingNonTrivial
14: [ OK ] TranslateAndScaleTest.scalingNonTrivial (0 ms)
14: [ RUN ] TranslateAndScaleTest.scalingInverseNoZero
14: [ OK ] TranslateAndScaleTest.scalingInverseNoZero (0 ms)
14: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero
14: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero (0 ms)
14: [----------] 8 tests from TranslateAndScaleTest (2 ms total)
14:
14: [----------] 12 tests from DensitySimilarityTest
14: [ RUN ] DensitySimilarityTest.InnerProductIsCorrect
14: [ OK ] DensitySimilarityTest.InnerProductIsCorrect (1 ms)
14: [ RUN ] DensitySimilarityTest.InnerProductGradientIsCorrect
14: [ OK ] DensitySimilarityTest.InnerProductGradientIsCorrect (0 ms)
14: [ RUN ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch
14: [ OK ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch (1 ms)
14: [ RUN ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch
14: [ OK ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch (0 ms)
14: [ RUN ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect
14: [ OK ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect (0 ms)
14: [ RUN ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero
14: [ OK ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero (0 ms)
14: [ RUN ] DensitySimilarityTest.RelativeEntropyIsCorrect
14: [ OK ] DensitySimilarityTest.RelativeEntropyIsCorrect (0 ms)
14: [ RUN ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect
14: [ OK ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect (2 ms)
14: [ RUN ] DensitySimilarityTest.CrossCorrelationIsOne
14: [ OK ] DensitySimilarityTest.CrossCorrelationIsOne (124 ms)
14: [ RUN ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated
14: [ OK ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated (134 ms)
14: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated
14: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated (123 ms)
14: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect
14: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect (7 ms)
14: [----------] 12 tests from DensitySimilarityTest (392 ms total)
14:
14: [----------] 6 tests from StructureSimilarityTest
14: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD
14: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD (1 ms)
14: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho
14: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho (0 ms)
14: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSD
14: [ OK ] StructureSimilarityTest.YieldsCorrectRMSD (0 ms)
14: [ RUN ] StructureSimilarityTest.YieldsCorrectRho
14: [ OK ] StructureSimilarityTest.YieldsCorrectRho (0 ms)
14: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex
14: [ OK ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex (0 ms)
14: [ RUN ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex
14: [ OK ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex (0 ms)
14: [----------] 6 tests from StructureSimilarityTest (1 ms total)
14:
14: [----------] 8 tests from ExponentialMovingAverage
14: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero
14: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero (0 ms)
14: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative
14: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative (1 ms)
14: [ RUN ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue
14: [ OK ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue (0 ms)
14: [ RUN ] ExponentialMovingAverage.YieldsCorrectValue
14: [ OK ] ExponentialMovingAverage.YieldsCorrectValue (0 ms)
14: [ RUN ] ExponentialMovingAverage.SetAverageCorrectly
14: [ OK ] ExponentialMovingAverage.SetAverageCorrectly (0 ms)
14: [ RUN ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing
14: [ OK ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing (0 ms)
14: [ RUN ] ExponentialMovingAverage.InverseLagTimeCorrect
14: [ OK ] ExponentialMovingAverage.InverseLagTimeCorrect (0 ms)
14: [ RUN ] ExponentialMovingAverage.RoundTripAsKeyValueTree
14: [ OK ] ExponentialMovingAverage.RoundTripAsKeyValueTree (0 ms)
14: [----------] 8 tests from ExponentialMovingAverage (1 ms total)
14:
14: [----------] 21 tests from FunctionTest
14: [ RUN ] FunctionTest.StaticLog2
14: [ OK ] FunctionTest.StaticLog2 (1 ms)
14: [ RUN ] FunctionTest.Log2I32Bit
14: [ OK ] FunctionTest.Log2I32Bit (1 ms)
14: [ RUN ] FunctionTest.Log2I64Bit
14: [ OK ] FunctionTest.Log2I64Bit (1 ms)
14: [ RUN ] FunctionTest.GreatestCommonDivisor
14: [ OK ] FunctionTest.GreatestCommonDivisor (0 ms)
14: [ RUN ] FunctionTest.InvsqrtFloat
14: [ OK ] FunctionTest.InvsqrtFloat (1 ms)
14: [ RUN ] FunctionTest.InvsqrtDouble
14: [ OK ] FunctionTest.InvsqrtDouble (0 ms)
14: [ RUN ] FunctionTest.InvsqrtInteger
14: [ OK ] FunctionTest.InvsqrtInteger (1 ms)
14: [ RUN ] FunctionTest.InvcbrtFloat
14: [ OK ] FunctionTest.InvcbrtFloat (1 ms)
14: [ RUN ] FunctionTest.InvcbrtDouble
14: [ OK ] FunctionTest.InvcbrtDouble (0 ms)
14: [ RUN ] FunctionTest.InvcbrtInteger
14: [ OK ] FunctionTest.InvcbrtInteger (1 ms)
14: [ RUN ] FunctionTest.SixthrootFloat
14: [ OK ] FunctionTest.SixthrootFloat (0 ms)
14: [ RUN ] FunctionTest.SixthrootDouble
14: [ OK ] FunctionTest.SixthrootDouble (1 ms)
14: [ RUN ] FunctionTest.SixthrootInteger
14: [ OK ] FunctionTest.SixthrootInteger (1 ms)
14: [ RUN ] FunctionTest.InvsixthrootFloat
14: [ OK ] FunctionTest.InvsixthrootFloat (0 ms)
14: [ RUN ] FunctionTest.InvsixthrootDouble
14: [ OK ] FunctionTest.InvsixthrootDouble (1 ms)
14: [ RUN ] FunctionTest.InvsixthrootInteger
14: [ OK ] FunctionTest.InvsixthrootInteger (1 ms)
14: [ RUN ] FunctionTest.Powers
14: [ OK ] FunctionTest.Powers (0 ms)
14: [ RUN ] FunctionTest.ErfInvFloat
14: [ OK ] FunctionTest.ErfInvFloat (0 ms)
14: [ RUN ] FunctionTest.ErfInvDouble
14: [ OK ] FunctionTest.ErfInvDouble (1 ms)
14: [ RUN ] FunctionTest.ErfAndErfInvAreInversesFloat
14: [ OK ] FunctionTest.ErfAndErfInvAreInversesFloat (1 ms)
14: [ RUN ] FunctionTest.ErfAndErfInvAreInversesDouble
14: [ OK ] FunctionTest.ErfAndErfInvAreInversesDouble (1 ms)
14: [----------] 21 tests from FunctionTest (14 ms total)
14:
14: [----------] 4 tests from GaussianOn1DLattice
14: [ RUN ] GaussianOn1DLattice.sumsCloseToOne
14: [ OK ] GaussianOn1DLattice.sumsCloseToOne (0 ms)
14: [ RUN ] GaussianOn1DLattice.isCorrect
14: [ OK ] GaussianOn1DLattice.isCorrect (1 ms)
14: [ RUN ] GaussianOn1DLattice.complementaryAmplitudesSumToZero
14: [ OK ] GaussianOn1DLattice.complementaryAmplitudesSumToZero (0 ms)
14: [ RUN ] GaussianOn1DLattice.doesNotOverflowForLargeRange
14: [ OK ] GaussianOn1DLattice.doesNotOverflowForLargeRange (0 ms)
14: [----------] 4 tests from GaussianOn1DLattice (1 ms total)
14:
14: [----------] 9 tests from GaussTransformTest
14: [ RUN ] GaussTransformTest.isZeroUponConstruction
14: [ OK ] GaussTransformTest.isZeroUponConstruction (0 ms)
14: [ RUN ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss
14: [ OK ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss (0 ms)
14: [ RUN ] GaussTransformTest.isZeroAfterSettingZero
14: [ OK ] GaussTransformTest.isZeroAfterSettingZero (0 ms)
14: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinX
14: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinX (0 ms)
14: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinY
14: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinY (0 ms)
14: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinZ
14: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinZ (0 ms)
14: [ RUN ] GaussTransformTest.complementaryGaussAddToZero
14: [ OK ] GaussTransformTest.complementaryGaussAddToZero (0 ms)
14: [ RUN ] GaussTransformTest.centerGaussianInCubeHasExpectedValues
14: [ OK ] GaussTransformTest.centerGaussianInCubeHasExpectedValues (0 ms)
14: [ RUN ] GaussTransformTest.view
14: [ OK ] GaussTransformTest.view (0 ms)
14: [----------] 9 tests from GaussTransformTest (1 ms total)
14:
14: [----------] 3 tests from DensityFittingForce
14: [ RUN ] DensityFittingForce.isZeroWhenMatchingDensity
14: [ OK ] DensityFittingForce.isZeroWhenMatchingDensity (0 ms)
14: [ RUN ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections
14: [ OK ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections (0 ms)
14: [ RUN ] DensityFittingForce.pullsTowardsDerivative
14: [ OK ] DensityFittingForce.pullsTowardsDerivative (0 ms)
14: [----------] 3 tests from DensityFittingForce (1 ms total)
14:
14: [----------] 2 tests from InvertMatrixTest
14: [ RUN ] InvertMatrixTest.IdentityIsImpotent
14: [ OK ] InvertMatrixTest.IdentityIsImpotent (0 ms)
14: [ RUN ] InvertMatrixTest.ComputesInverse
14: [ OK ] InvertMatrixTest.ComputesInverse (0 ms)
14: [----------] 2 tests from InvertMatrixTest (0 ms total)
14:
14: [----------] 2 tests from InvertBoxMatrixTest
14: [ RUN ] InvertBoxMatrixTest.IdentityIsImpotent
14: [ OK ] InvertBoxMatrixTest.IdentityIsImpotent (0 ms)
14: [ RUN ] InvertBoxMatrixTest.ComputesInverseInPlace
14: [ OK ] InvertBoxMatrixTest.ComputesInverseInPlace (0 ms)
14: [----------] 2 tests from InvertBoxMatrixTest (0 ms total)
14:
14: [----------] 15 tests from MatrixTest
14: [ RUN ] MatrixTest.canSetFromArray
14: [ OK ] MatrixTest.canSetFromArray (0 ms)
14: [ RUN ] MatrixTest.canSetStaticallyFromList
14: [ OK ] MatrixTest.canSetStaticallyFromList (0 ms)
14: [ RUN ] MatrixTest.canConstructAndFill
14: [ OK ] MatrixTest.canConstructAndFill (0 ms)
14: [ RUN ] MatrixTest.canSetValues
14: [ OK ] MatrixTest.canSetValues (0 ms)
14: [ RUN ] MatrixTest.canCopyAssign
14: [ OK ] MatrixTest.canCopyAssign (1 ms)
14: [ RUN ] MatrixTest.canSwap
14: [ OK ] MatrixTest.canSwap (0 ms)
14: [ RUN ] MatrixTest.staticMultiDimArrayExtent
14: [ OK ] MatrixTest.staticMultiDimArrayExtent (0 ms)
14: [ RUN ] MatrixTest.determinantWorks
14: [ OK ] MatrixTest.determinantWorks (0 ms)
14: [ RUN ] MatrixTest.noninvertableDeterminantIsZero
14: [ OK ] MatrixTest.noninvertableDeterminantIsZero (0 ms)
14: [ RUN ] MatrixTest.determinantOfDiagonalMatrix
14: [ OK ] MatrixTest.determinantOfDiagonalMatrix (0 ms)
14: [ RUN ] MatrixTest.traceWorks
14: [ OK ] MatrixTest.traceWorks (0 ms)
14: [ RUN ] MatrixTest.transposeWorks
14: [ OK ] MatrixTest.transposeWorks (0 ms)
14: [ RUN ] MatrixTest.transposeOfSymmetricMatrix
14: [ OK ] MatrixTest.transposeOfSymmetricMatrix (0 ms)
14: [ RUN ] MatrixTest.canCreateFromLegacyMatrix
14: [ OK ] MatrixTest.canCreateFromLegacyMatrix (0 ms)
14: [ RUN ] MatrixTest.canFillLegacyMatrix
14: [ OK ] MatrixTest.canFillLegacyMatrix (0 ms)
14: [----------] 15 tests from MatrixTest (1 ms total)
14:
14: [----------] 25 tests from MultiDimArrayTest
14: [ RUN ] MultiDimArrayTest.canConstructAndFillStatic
14: [ OK ] MultiDimArrayTest.canConstructAndFillStatic (0 ms)
14: [ RUN ] MultiDimArrayTest.canConstructAndFillDynamic
14: [ OK ] MultiDimArrayTest.canConstructAndFillDynamic (0 ms)
14: [ RUN ] MultiDimArrayTest.canSetValuesInStatic
14: [ OK ] MultiDimArrayTest.canSetValuesInStatic (0 ms)
14: [ RUN ] MultiDimArrayTest.canSetValuesInDynamic
14: [ OK ] MultiDimArrayTest.canSetValuesInDynamic (0 ms)
14: [ RUN ] MultiDimArrayTest.canMoveConstructStatic
14: [ OK ] MultiDimArrayTest.canMoveConstructStatic (0 ms)
14: [ RUN ] MultiDimArrayTest.canMoveConstructDynamic
14: [ OK ] MultiDimArrayTest.canMoveConstructDynamic (0 ms)
14: [ RUN ] MultiDimArrayTest.canMoveAssignStatic
14: [ OK ] MultiDimArrayTest.canMoveAssignStatic (0 ms)
14: [ RUN ] MultiDimArrayTest.canMoveAssignDynamic
14: [ OK ] MultiDimArrayTest.canMoveAssignDynamic (0 ms)
14: [ RUN ] MultiDimArrayTest.canCopyConstructStatic
14: [ OK ] MultiDimArrayTest.canCopyConstructStatic (0 ms)
14: [ RUN ] MultiDimArrayTest.canCopyConstructDynamic
14: [ OK ] MultiDimArrayTest.canCopyConstructDynamic (0 ms)
14: [ RUN ] MultiDimArrayTest.canCopyAssignStatic
14: [ OK ] MultiDimArrayTest.canCopyAssignStatic (0 ms)
14: [ RUN ] MultiDimArrayTest.canCopyAssignDynamic
14: [ OK ] MultiDimArrayTest.canCopyAssignDynamic (0 ms)
14: [ RUN ] MultiDimArrayTest.canSwapStatic
14: [ OK ] MultiDimArrayTest.canSwapStatic (0 ms)
14: [ RUN ] MultiDimArrayTest.canSwapDynamic
14: [ OK ] MultiDimArrayTest.canSwapDynamic (0 ms)
14: [ RUN ] MultiDimArrayTest.staticMultiDimArrayExtent
14: [ OK ] MultiDimArrayTest.staticMultiDimArrayExtent (0 ms)
14: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayExtent
14: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayExtent (0 ms)
14: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent
14: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent (0 ms)
14: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue
14: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue (0 ms)
14: [ RUN ] MultiDimArrayTest.staticMultiDimArrayFromArray
14: [ OK ] MultiDimArrayTest.staticMultiDimArrayFromArray (0 ms)
14: [ RUN ] MultiDimArrayTest.conversionToView
14: [ OK ] MultiDimArrayTest.conversionToView (0 ms)
14: [ RUN ] MultiDimArrayTest.conversionToConstView
14: [ OK ] MultiDimArrayTest.conversionToConstView (0 ms)
14: [ RUN ] MultiDimArrayTest.viewBegin
14: [ OK ] MultiDimArrayTest.viewBegin (0 ms)
14: [ RUN ] MultiDimArrayTest.viewEnd
14: [ OK ] MultiDimArrayTest.viewEnd (0 ms)
14: [ RUN ] MultiDimArrayTest.constViewConstBegin
14: [ OK ] MultiDimArrayTest.constViewConstBegin (0 ms)
14: [ RUN ] MultiDimArrayTest.constViewConstEnd
14: [ OK ] MultiDimArrayTest.constViewConstEnd (0 ms)
14: [----------] 25 tests from MultiDimArrayTest (1 ms total)
14:
14: [----------] 4 tests from MultiDimArrayToMdSpanTest
14: [ RUN ] MultiDimArrayToMdSpanTest.convertsToMdSpan
14: [ OK ] MultiDimArrayToMdSpanTest.convertsToMdSpan (0 ms)
14: [ RUN ] MultiDimArrayToMdSpanTest.constArrayToMdSpan
14: [ OK ] MultiDimArrayToMdSpanTest.constArrayToMdSpan (0 ms)
14: [ RUN ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan
14: [ OK ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan (0 ms)
14: [ RUN ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan
14: [ OK ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan (0 ms)
14: [----------] 4 tests from MultiDimArrayToMdSpanTest (1 ms total)
14:
14: [----------] 4 tests from PaddedVectorTest/0, where TypeParam = std::allocator<int>
14: [ RUN ] PaddedVectorTest/0.ConstructsResizesAndReserves
14: [ OK ] PaddedVectorTest/0.ConstructsResizesAndReserves (0 ms)
14: [ RUN ] PaddedVectorTest/0.CanCopyAssign
14: [ OK ] PaddedVectorTest/0.CanCopyAssign (0 ms)
14: [ RUN ] PaddedVectorTest/0.CanMoveAssign
14: [ OK ] PaddedVectorTest/0.CanMoveAssign (0 ms)
14: [ RUN ] PaddedVectorTest/0.CanSwap
14: [ OK ] PaddedVectorTest/0.CanSwap (0 ms)
14: [----------] 4 tests from PaddedVectorTest/0 (0 ms total)
14:
14: [----------] 4 tests from PaddedVectorTest/1, where TypeParam = std::allocator<float>
14: [ RUN ] PaddedVectorTest/1.ConstructsResizesAndReserves
14: [ OK ] PaddedVectorTest/1.ConstructsResizesAndReserves (0 ms)
14: [ RUN ] PaddedVectorTest/1.CanCopyAssign
14: [ OK ] PaddedVectorTest/1.CanCopyAssign (0 ms)
14: [ RUN ] PaddedVectorTest/1.CanMoveAssign
14: [ OK ] PaddedVectorTest/1.CanMoveAssign (0 ms)
14: [ RUN ] PaddedVectorTest/1.CanSwap
14: [ OK ] PaddedVectorTest/1.CanSwap (0 ms)
14: [----------] 4 tests from PaddedVectorTest/1 (0 ms total)
14:
14: [----------] 4 tests from PaddedVectorTest/2, where TypeParam = std::allocator<double>
14: [ RUN ] PaddedVectorTest/2.ConstructsResizesAndReserves
14: [ OK ] PaddedVectorTest/2.ConstructsResizesAndReserves (0 ms)
14: [ RUN ] PaddedVectorTest/2.CanCopyAssign
14: [ OK ] PaddedVectorTest/2.CanCopyAssign (0 ms)
14: [ RUN ] PaddedVectorTest/2.CanMoveAssign
14: [ OK ] PaddedVectorTest/2.CanMoveAssign (0 ms)
14: [ RUN ] PaddedVectorTest/2.CanSwap
14: [ OK ] PaddedVectorTest/2.CanSwap (0 ms)
14: [----------] 4 tests from PaddedVectorTest/2 (1 ms total)
14:
14: [----------] 4 tests from PaddedVectorTest/3, where TypeParam = std::allocator<gmx::BasicVector<float> >
14: [ RUN ] PaddedVectorTest/3.ConstructsResizesAndReserves
14: [ OK ] PaddedVectorTest/3.ConstructsResizesAndReserves (0 ms)
14: [ RUN ] PaddedVectorTest/3.CanCopyAssign
14: [ OK ] PaddedVectorTest/3.CanCopyAssign (0 ms)
14: [ RUN ] PaddedVectorTest/3.CanMoveAssign
14: [ OK ] PaddedVectorTest/3.CanMoveAssign (0 ms)
14: [ RUN ] PaddedVectorTest/3.CanSwap
14: [ OK ] PaddedVectorTest/3.CanSwap (0 ms)
14: [----------] 4 tests from PaddedVectorTest/3 (0 ms total)
14:
14: [----------] 4 tests from PaddedVectorTest/4, where TypeParam = std::allocator<gmx::BasicVector<double> >
14: [ RUN ] PaddedVectorTest/4.ConstructsResizesAndReserves
14: [ OK ] PaddedVectorTest/4.ConstructsResizesAndReserves (0 ms)
14: [ RUN ] PaddedVectorTest/4.CanCopyAssign
14: [ OK ] PaddedVectorTest/4.CanCopyAssign (0 ms)
14: [ RUN ] PaddedVectorTest/4.CanMoveAssign
14: [ OK ] PaddedVectorTest/4.CanMoveAssign (0 ms)
14: [ RUN ] PaddedVectorTest/4.CanSwap
14: [ OK ] PaddedVectorTest/4.CanSwap (0 ms)
14: [----------] 4 tests from PaddedVectorTest/4 (0 ms total)
14:
14: [----------] 4 tests from PaddedVectorTest/5, where TypeParam = gmx::Allocator<int, gmx::AlignedAllocationPolicy>
14: [ RUN ] PaddedVectorTest/5.ConstructsResizesAndReserves
14: [ OK ] PaddedVectorTest/5.ConstructsResizesAndReserves (0 ms)
14: [ RUN ] PaddedVectorTest/5.CanCopyAssign
14: [ OK ] PaddedVectorTest/5.CanCopyAssign (0 ms)
14: [ RUN ] PaddedVectorTest/5.CanMoveAssign
14: [ OK ] PaddedVectorTest/5.CanMoveAssign (0 ms)
14: [ RUN ] PaddedVectorTest/5.CanSwap
14: [ OK ] PaddedVectorTest/5.CanSwap (0 ms)
14: [----------] 4 tests from PaddedVectorTest/5 (1 ms total)
14:
14: [----------] 4 tests from PaddedVectorTest/6, where TypeParam = gmx::Allocator<float, gmx::AlignedAllocationPolicy>
14: [ RUN ] PaddedVectorTest/6.ConstructsResizesAndReserves
14: [ OK ] PaddedVectorTest/6.ConstructsResizesAndReserves (0 ms)
14: [ RUN ] PaddedVectorTest/6.CanCopyAssign
14: [ OK ] PaddedVectorTest/6.CanCopyAssign (0 ms)
14: [ RUN ] PaddedVectorTest/6.CanMoveAssign
14: [ OK ] PaddedVectorTest/6.CanMoveAssign (0 ms)
14: [ RUN ] PaddedVectorTest/6.CanSwap
14: [ OK ] PaddedVectorTest/6.CanSwap (0 ms)
14: [----------] 4 tests from PaddedVectorTest/6 (0 ms total)
14:
14: [----------] 4 tests from PaddedVectorTest/7, where TypeParam = gmx::Allocator<double, gmx::AlignedAllocationPolicy>
14: [ RUN ] PaddedVectorTest/7.ConstructsResizesAndReserves
14: [ OK ] PaddedVectorTest/7.ConstructsResizesAndReserves (0 ms)
14: [ RUN ] PaddedVectorTest/7.CanCopyAssign
14: [ OK ] PaddedVectorTest/7.CanCopyAssign (0 ms)
14: [ RUN ] PaddedVectorTest/7.CanMoveAssign
14: [ OK ] PaddedVectorTest/7.CanMoveAssign (0 ms)
14: [ RUN ] PaddedVectorTest/7.CanSwap
14: [ OK ] PaddedVectorTest/7.CanSwap (0 ms)
14: [----------] 4 tests from PaddedVectorTest/7 (1 ms total)
14:
14: [----------] 4 tests from PaddedVectorTest/8, where TypeParam = gmx::Allocator<gmx::BasicVector<float>, gmx::AlignedAllocationPolicy>
14: [ RUN ] PaddedVectorTest/8.ConstructsResizesAndReserves
14: [ OK ] PaddedVectorTest/8.ConstructsResizesAndReserves (0 ms)
14: [ RUN ] PaddedVectorTest/8.CanCopyAssign
14: [ OK ] PaddedVectorTest/8.CanCopyAssign (0 ms)
14: [ RUN ] PaddedVectorTest/8.CanMoveAssign
14: [ OK ] PaddedVectorTest/8.CanMoveAssign (0 ms)
14: [ RUN ] PaddedVectorTest/8.CanSwap
14: [ OK ] PaddedVectorTest/8.CanSwap (0 ms)
14: [----------] 4 tests from PaddedVectorTest/8 (0 ms total)
14:
14: [----------] 4 tests from PaddedVectorTest/9, where TypeParam = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>
14: [ RUN ] PaddedVectorTest/9.ConstructsResizesAndReserves
14: [ OK ] PaddedVectorTest/9.ConstructsResizesAndReserves (0 ms)
14: [ RUN ] PaddedVectorTest/9.CanCopyAssign
14: [ OK ] PaddedVectorTest/9.CanCopyAssign (0 ms)
14: [ RUN ] PaddedVectorTest/9.CanMoveAssign
14: [ OK ] PaddedVectorTest/9.CanMoveAssign (0 ms)
14: [ RUN ] PaddedVectorTest/9.CanSwap
14: [ OK ] PaddedVectorTest/9.CanSwap (0 ms)
14: [----------] 4 tests from PaddedVectorTest/9 (0 ms total)
14:
14: [----------] 37 tests from RVecTest
14: [ RUN ] RVecTest.CanBeStoredInVector
14: [ OK ] RVecTest.CanBeStoredInVector (0 ms)
14: [ RUN ] RVecTest.ConvertsImplicitlyFrom_rvec
14: [ OK ] RVecTest.ConvertsImplicitlyFrom_rvec (0 ms)
14: [ RUN ] RVecTest.ConvertsImplicitlyTo_rvec
14: [ OK ] RVecTest.ConvertsImplicitlyTo_rvec (0 ms)
14: [ RUN ] RVecTest.WorksAsMutable_rvec
14: [ OK ] RVecTest.WorksAsMutable_rvec (0 ms)
14: [ RUN ] RVecTest.WorksAs_rvec_Array
14: [ OK ] RVecTest.WorksAs_rvec_Array (0 ms)
14: [ RUN ] RVecTest.CanAddRVecToRvec
14: [ OK ] RVecTest.CanAddRVecToRvec (0 ms)
14: [ RUN ] RVecTest.CanAddAssignRVecToRvec
14: [ OK ] RVecTest.CanAddAssignRVecToRvec (0 ms)
14: [ RUN ] RVecTest.CanSubtractRVecFromRvec
14: [ OK ] RVecTest.CanSubtractRVecFromRvec (0 ms)
14: [ RUN ] RVecTest.CanSubtractAssignRVecFromRvec
14: [ OK ] RVecTest.CanSubtractAssignRVecFromRvec (0 ms)
14: [ RUN ] RVecTest.CanDotProductRVecByRvec
14: [ OK ] RVecTest.CanDotProductRVecByRvec (0 ms)
14: [ RUN ] RVecTest.CanCrossProductRVecByRvec
14: [ OK ] RVecTest.CanCrossProductRVecByRvec (0 ms)
14: [ RUN ] RVecTest.CanDivideRVecInplace
14: [ OK ] RVecTest.CanDivideRVecInplace (0 ms)
14: [ RUN ] RVecTest.CanScaleRVec
14: [ OK ] RVecTest.CanScaleRVec (0 ms)
14: [ RUN ] RVecTest.CanDivideRVec
14: [ OK ] RVecTest.CanDivideRVec (0 ms)
14: [ RUN ] RVecTest.CanDoUnitvFromRVec
14: [ OK ] RVecTest.CanDoUnitvFromRVec (0 ms)
14: [ RUN ] RVecTest.CanSqLengthOfRVec
14: [ OK ] RVecTest.CanSqLengthOfRVec (0 ms)
14: [ RUN ] RVecTest.CanLengthOfRVec
14: [ OK ] RVecTest.CanLengthOfRVec (0 ms)
14: [ RUN ] RVecTest.CanCastToRVec
14: [ OK ] RVecTest.CanCastToRVec (0 ms)
14: [ RUN ] RVecTest.CanCastToDVec
14: [ OK ] RVecTest.CanCastToDVec (0 ms)
14: [ RUN ] RVecTest.CanLeftScalarMultiply
14: [ OK ] RVecTest.CanLeftScalarMultiply (0 ms)
14: [ RUN ] RVecTest.CanRightScalarMultiply
14: [ OK ] RVecTest.CanRightScalarMultiply (0 ms)
14: [ RUN ] RVecTest.CanGetUnitvFromRVec
14: [ OK ] RVecTest.CanGetUnitvFromRVec (0 ms)
14: [ RUN ] RVecTest.CanGetSqLengthOfRVec
14: [ OK ] RVecTest.CanGetSqLengthOfRVec (0 ms)
14: [ RUN ] RVecTest.CanGetLengthOfRVec
14: [ OK ] RVecTest.CanGetLengthOfRVec (0 ms)
14: [ RUN ] RVecTest.CanDoCrossProductOfRVec
14: [ OK ] RVecTest.CanDoCrossProductOfRVec (0 ms)
14: [ RUN ] RVecTest.CanDoDotProductOfRVec
14: [ OK ] RVecTest.CanDoDotProductOfRVec (0 ms)
14: [ RUN ] RVecTest.CanScaleByVector
14: [ OK ] RVecTest.CanScaleByVector (0 ms)
14: [ RUN ] RVecTest.asIVec
14: [ OK ] RVecTest.asIVec (0 ms)
14: [ RUN ] RVecTest.elementWiseMin
14: [ OK ] RVecTest.elementWiseMin (0 ms)
14: [ RUN ] RVecTest.elementWiseMax
14: [ OK ] RVecTest.elementWiseMax (0 ms)
14: [ RUN ] RVecTest.WorksAs_dvec_Reference
14: [ OK ] RVecTest.WorksAs_dvec_Reference (0 ms)
14: [ RUN ] RVecTest.WorksAs_ivec_Reference
14: [ OK ] RVecTest.WorksAs_ivec_Reference (0 ms)
14: [ RUN ] RVecTest.WorksAs_rvec_Reference
14: [ OK ] RVecTest.WorksAs_rvec_Reference (0 ms)
14: [ RUN ] RVecTest.CopyConstructorWorks
14: [ OK ] RVecTest.CopyConstructorWorks (0 ms)
14: [ RUN ] RVecTest.CopyAssignmentWorks
14: [ OK ] RVecTest.CopyAssignmentWorks (0 ms)
14: [ RUN ] RVecTest.MoveConstructorWorks
14: [ OK ] RVecTest.MoveConstructorWorks (0 ms)
14: [ RUN ] RVecTest.MoveAssignmentWorks
14: [ OK ] RVecTest.MoveAssignmentWorks (0 ms)
14: [----------] 37 tests from RVecTest (2 ms total)
14:
14: [----------] Global test environment tear-down
14: [==========] 204 tests from 29 test cases ran. (422 ms total)
14: [ PASSED ] 204 tests.
14/52 Test #14: MathUnitTests ....................... Passed 0.51 sec
test 15
Start 15: MdrunUtilityUnitTests
15: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrunutility-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunUtilityUnitTests.xml"
15: Test timeout computed to be: 30
15: [==========] Running 17 tests from 1 test case.
15: [----------] Global test environment set-up.
15: [----------] 17 tests from ThreadAffinityTest
15: [ RUN ] ThreadAffinityTest.DoesNothingWhenDisabled
15: [ OK ] ThreadAffinityTest.DoesNothingWhenDisabled (1 ms)
15: [ RUN ] ThreadAffinityTest.DoesNothingWhenNotSupported
15: [ OK ] ThreadAffinityTest.DoesNothingWhenNotSupported (0 ms)
15: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads
15: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads (1 ms)
15: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads
15: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads (1 ms)
15: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads
15: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads (0 ms)
15: [ RUN ] ThreadAffinityTest.DoesNothingWithUnknownHardware
15: [ OK ] ThreadAffinityTest.DoesNothingWithUnknownHardware (1 ms)
15: [ RUN ] ThreadAffinityTest.DoesNothingWithTooManyThreads
15: [ OK ] ThreadAffinityTest.DoesNothingWithTooManyThreads (0 ms)
15: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeOffset
15: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeOffset (2 ms)
15: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeStride
15: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeStride (0 ms)
15: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithAuto
15: [ OK ] ThreadAffinityTest.PinsSingleThreadWithAuto (1 ms)
15: [ RUN ] ThreadAffinityTest.PinsSingleThreadWhenForced
15: [ OK ] ThreadAffinityTest.PinsSingleThreadWhenForced (1 ms)
15: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced
15: [ OK ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced (1 ms)
15: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread
15: NOTE: Affinity setting failed.
15: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread (2 ms)
15: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithAuto
15: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithAuto (1 ms)
15: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced
15: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced (1 ms)
15: [ RUN ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads
15: [ OK ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads (2 ms)
15: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing
15: NOTE: Affinity setting for 1/2 threads failed.
15: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing (2 ms)
15: [----------] 17 tests from ThreadAffinityTest (18 ms total)
15:
15: [----------] Global test environment tear-down
15: [==========] 17 tests from 1 test case ran. (18 ms total)
15: [ PASSED ] 17 tests.
15/52 Test #15: MdrunUtilityUnitTests ............... Passed 0.08 sec
test 16
Start 16: MdrunUtilityMpiUnitTests
16: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrunutility-mpi-test "-ntmpi" "4" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunUtilityMpiUnitTests.xml"
16: Test timeout computed to be: 30
16: [==========] Running 13 tests from 2 test cases.
16: [----------] Global test environment set-up.
16: [----------] 6 tests from ThreadAffinityMultiRankTest
16: [ RUN ] ThreadAffinityMultiRankTest.PinsWholeNode
16: [ OK ] ThreadAffinityMultiRankTest.PinsWholeNode (51 ms)
16: [ RUN ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride
16: [ OK ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride (11 ms)
16: [ RUN ] ThreadAffinityMultiRankTest.PinsTwoNodes
16: [ OK ] ThreadAffinityMultiRankTest.PinsTwoNodes (4 ms)
16: [ RUN ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled
16: [ OK ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled (1 ms)
16: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto
16: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto (2 ms)
16: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce
16: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce (2 ms)
16: [----------] 6 tests from ThreadAffinityMultiRankTest (76 ms total)
16:
16: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest
16: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly
16: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly (4 ms)
16: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly
16: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly (3 ms)
16: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster
16: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster (4 ms)
16: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly
16: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly (3 ms)
16: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly
16: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly (4 ms)
16: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly
16: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly (5 ms)
16: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly
16: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly (4 ms)
16: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest (31 ms total)
16:
16: [----------] Global test environment tear-down
16: [==========] 13 tests from 2 test cases ran. (109 ms total)
16: [ PASSED ] 13 tests.
16/52 Test #16: MdrunUtilityMpiUnitTests ............ Passed 0.17 sec
test 17
Start 17: MDSpanTests
17: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdspan-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MDSpanTests.xml"
17: Test timeout computed to be: 30
17: [==========] Running 32 tests from 7 test cases.
17: [----------] Global test environment set-up.
17: [----------] 4 tests from BasicAccessorPolicy
17: [ RUN ] BasicAccessorPolicy.Decay
17: [ OK ] BasicAccessorPolicy.Decay (0 ms)
17: [ RUN ] BasicAccessorPolicy.Access
17: [ OK ] BasicAccessorPolicy.Access (0 ms)
17: [ RUN ] BasicAccessorPolicy.Offset
17: [ OK ] BasicAccessorPolicy.Offset (0 ms)
17: [ RUN ] BasicAccessorPolicy.CopyAccessor
17: [ OK ] BasicAccessorPolicy.CopyAccessor (0 ms)
17: [----------] 4 tests from BasicAccessorPolicy (1 ms total)
17:
17: [----------] 4 tests from ExtentsTest
17: [ RUN ] ExtentsTest.Construction
17: [ OK ] ExtentsTest.Construction (0 ms)
17: [ RUN ] ExtentsTest.PurelyStatic
17: [ OK ] ExtentsTest.PurelyStatic (0 ms)
17: [ RUN ] ExtentsTest.RankNought
17: [ OK ] ExtentsTest.RankNought (0 ms)
17: [ RUN ] ExtentsTest.Assignment
17: [ OK ] ExtentsTest.Assignment (0 ms)
17: [----------] 4 tests from ExtentsTest (1 ms total)
17:
17: [----------] 8 tests from MdSpanExtension
17: [ RUN ] MdSpanExtension.SlicingAllStatic
17: [ OK ] MdSpanExtension.SlicingAllStatic (0 ms)
17: [ RUN ] MdSpanExtension.SlicingDynamic
17: [ OK ] MdSpanExtension.SlicingDynamic (0 ms)
17: [ RUN ] MdSpanExtension.SlicingAllStatic3D
17: [ OK ] MdSpanExtension.SlicingAllStatic3D (0 ms)
17: [ RUN ] MdSpanExtension.SlicingEqualsView3D
17: [ OK ] MdSpanExtension.SlicingEqualsView3D (0 ms)
17: [ RUN ] MdSpanExtension.additionWorks
17: [ OK ] MdSpanExtension.additionWorks (0 ms)
17: [ RUN ] MdSpanExtension.subtractionWorks
17: [ OK ] MdSpanExtension.subtractionWorks (0 ms)
17: [ RUN ] MdSpanExtension.multiplicationWorks
17: [ OK ] MdSpanExtension.multiplicationWorks (0 ms)
17: [ RUN ] MdSpanExtension.divisionWorks
17: [ OK ] MdSpanExtension.divisionWorks (0 ms)
17: [----------] 8 tests from MdSpanExtension (2 ms total)
17:
17: [----------] 3 tests from LayoutTests
17: [ RUN ] LayoutTests.LayoutRightConstruction
17: [ OK ] LayoutTests.LayoutRightConstruction (0 ms)
17: [ RUN ] LayoutTests.LayoutRightProperties
17: [ OK ] LayoutTests.LayoutRightProperties (0 ms)
17: [ RUN ] LayoutTests.LayoutRightOperator
17: [ OK ] LayoutTests.LayoutRightOperator (0 ms)
17: [----------] 3 tests from LayoutTests (1 ms total)
17:
17: [----------] 1 test from MdSpanTest
17: [ RUN ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly
17: [ OK ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly (0 ms)
17: [----------] 1 test from MdSpanTest (0 ms total)
17:
17: [----------] 6 tests from MdSpanTest/0, where TypeParam = gmx::basic_mdspan<int, gmx::extents<5, -1, 3, -1, 1>, gmx::layout_right, gmx::accessor_basic<int> >
17: [ RUN ] MdSpanTest/0.Rank
17: [ OK ] MdSpanTest/0.Rank (0 ms)
17: [ RUN ] MdSpanTest/0.DynamicRank
17: [ OK ] MdSpanTest/0.DynamicRank (0 ms)
17: [ RUN ] MdSpanTest/0.Extents
17: [ OK ] MdSpanTest/0.Extents (0 ms)
17: [ RUN ] MdSpanTest/0.Strides
17: [ OK ] MdSpanTest/0.Strides (0 ms)
17: [ RUN ] MdSpanTest/0.Properties
17: [ OK ] MdSpanTest/0.Properties (0 ms)
17: [ RUN ] MdSpanTest/0.Operator
17: [ OK ] MdSpanTest/0.Operator (0 ms)
17: [----------] 6 tests from MdSpanTest/0 (2 ms total)
17:
17: [----------] 6 tests from MdSpanTest/1, where TypeParam = gmx::basic_mdspan<float, gmx::extents<5, -1, 3, -1, 1>, gmx::layout_right, gmx::accessor_basic<float> >
17: [ RUN ] MdSpanTest/1.Rank
17: [ OK ] MdSpanTest/1.Rank (0 ms)
17: [ RUN ] MdSpanTest/1.DynamicRank
17: [ OK ] MdSpanTest/1.DynamicRank (0 ms)
17: [ RUN ] MdSpanTest/1.Extents
17: [ OK ] MdSpanTest/1.Extents (0 ms)
17: [ RUN ] MdSpanTest/1.Strides
17: [ OK ] MdSpanTest/1.Strides (0 ms)
17: [ RUN ] MdSpanTest/1.Properties
17: [ OK ] MdSpanTest/1.Properties (0 ms)
17: [ RUN ] MdSpanTest/1.Operator
17: [ OK ] MdSpanTest/1.Operator (0 ms)
17: [----------] 6 tests from MdSpanTest/1 (2 ms total)
17:
17: [----------] Global test environment tear-down
17: [==========] 32 tests from 7 test cases ran. (11 ms total)
17: [ PASSED ] 32 tests.
17/52 Test #17: MDSpanTests ......................... Passed 0.08 sec
test 18
Start 18: OnlineHelpUnitTests
18: Test command: /<<PKGBUILDDIR>>/build/basic/bin/onlinehelp-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/OnlineHelpUnitTests.xml"
18: Test timeout computed to be: 30
18: [==========] Running 22 tests from 4 test cases.
18: [----------] Global test environment set-up.
18: [----------] 6 tests from TextTableFormatterTest
18: [ RUN ] TextTableFormatterTest.HandlesBasicCase
18: [ OK ] TextTableFormatterTest.HandlesBasicCase (14 ms)
18: [ RUN ] TextTableFormatterTest.HandlesEmptyColumnTitles
18: [ OK ] TextTableFormatterTest.HandlesEmptyColumnTitles (1 ms)
18: [ RUN ] TextTableFormatterTest.HandlesIndentation
18: [ OK ] TextTableFormatterTest.HandlesIndentation (1 ms)
18: [ RUN ] TextTableFormatterTest.HandlesOverflowingLines
18: [ OK ] TextTableFormatterTest.HandlesOverflowingLines (1 ms)
18: [ RUN ] TextTableFormatterTest.HandlesLastColumnFolding
18: [ OK ] TextTableFormatterTest.HandlesLastColumnFolding (1 ms)
18: [ RUN ] TextTableFormatterTest.HandlesEmptyColumns
18: [ OK ] TextTableFormatterTest.HandlesEmptyColumns (1 ms)
18: [----------] 6 tests from TextTableFormatterTest (19 ms total)
18:
18: [----------] 3 tests from HelpManagerTest
18: [ RUN ] HelpManagerTest.HandlesRootTopic
18: [ OK ] HelpManagerTest.HandlesRootTopic (1 ms)
18: [ RUN ] HelpManagerTest.HandlesSubTopics
18: [ OK ] HelpManagerTest.HandlesSubTopics (0 ms)
18: [ RUN ] HelpManagerTest.HandlesInvalidTopics
18: [ OK ] HelpManagerTest.HandlesInvalidTopics (1 ms)
18: [----------] 3 tests from HelpManagerTest (2 ms total)
18:
18: [----------] 2 tests from HelpTopicFormattingTest
18: [ RUN ] HelpTopicFormattingTest.FormatsSimpleTopic
18: [ OK ] HelpTopicFormattingTest.FormatsSimpleTopic (1 ms)
18: [ RUN ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics
18: [ OK ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics (1 ms)
18: [----------] 2 tests from HelpTopicFormattingTest (2 ms total)
18:
18: [----------] 11 tests from HelpWriterContextTest
18: [ RUN ] HelpWriterContextTest.FormatsParagraphs
18: [ OK ] HelpWriterContextTest.FormatsParagraphs (0 ms)
18: [ RUN ] HelpWriterContextTest.FormatsRstStyleParagraphs
18: [ OK ] HelpWriterContextTest.FormatsRstStyleParagraphs (1 ms)
18: [ RUN ] HelpWriterContextTest.CleansUpExtraWhitespace
18: [ OK ] HelpWriterContextTest.CleansUpExtraWhitespace (1 ms)
18: [ RUN ] HelpWriterContextTest.FormatsLiteralText
18: [ OK ] HelpWriterContextTest.FormatsLiteralText (0 ms)
18: [ RUN ] HelpWriterContextTest.FormatsLiteralTextAtBeginning
18: [ OK ] HelpWriterContextTest.FormatsLiteralTextAtBeginning (1 ms)
18: [ RUN ] HelpWriterContextTest.FormatsLiteralTextWithIndentation
18: [ OK ] HelpWriterContextTest.FormatsLiteralTextWithIndentation (1 ms)
18: [ RUN ] HelpWriterContextTest.FormatsBulletList
18: [ OK ] HelpWriterContextTest.FormatsBulletList (1 ms)
18: [ RUN ] HelpWriterContextTest.FormatsEnumeratedList
18: [ OK ] HelpWriterContextTest.FormatsEnumeratedList (0 ms)
18: [ RUN ] HelpWriterContextTest.FormatsSimpleTable
18: [ OK ] HelpWriterContextTest.FormatsSimpleTable (1 ms)
18: [ RUN ] HelpWriterContextTest.FormatsGridTable
18: [ OK ] HelpWriterContextTest.FormatsGridTable (1 ms)
18: [ RUN ] HelpWriterContextTest.FormatsTitles
18: [ OK ] HelpWriterContextTest.FormatsTitles (0 ms)
18: [----------] 11 tests from HelpWriterContextTest (8 ms total)
18:
18: [----------] Global test environment tear-down
18: [==========] 22 tests from 4 test cases ran. (31 ms total)
18: [ PASSED ] 22 tests.
18/52 Test #18: OnlineHelpUnitTests ................. Passed 0.10 sec
test 19
Start 19: OptionsUnitTests
19: Test command: /<<PKGBUILDDIR>>/build/basic/bin/options-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/OptionsUnitTests.xml"
19: Test timeout computed to be: 30
19: [==========] Running 110 tests from 18 test cases.
19: [----------] Global test environment set-up.
19: [----------] 5 tests from AbstractOptionStorageTest
19: [ RUN ] AbstractOptionStorageTest.HandlesSetInFinish
19: [ OK ] AbstractOptionStorageTest.HandlesSetInFinish (1 ms)
19: [ RUN ] AbstractOptionStorageTest.HandlesValueRemoval
19: [ OK ] AbstractOptionStorageTest.HandlesValueRemoval (1 ms)
19: [ RUN ] AbstractOptionStorageTest.HandlesValueAddition
19: [ OK ] AbstractOptionStorageTest.HandlesValueAddition (1 ms)
19: [ RUN ] AbstractOptionStorageTest.HandlesTooManyValueAddition
19: [ OK ] AbstractOptionStorageTest.HandlesTooManyValueAddition (1 ms)
19: [ RUN ] AbstractOptionStorageTest.AllowsEmptyValues
19: [ OK ] AbstractOptionStorageTest.AllowsEmptyValues (0 ms)
19: [----------] 5 tests from AbstractOptionStorageTest (4 ms total)
19:
19: [----------] 8 tests from FileNameOptionTest
19: [ RUN ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension
19: [ OK ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension (0 ms)
19: [ RUN ] FileNameOptionTest.HandlesRequiredOptionWithoutValue
19: [ OK ] FileNameOptionTest.HandlesRequiredOptionWithoutValue (0 ms)
19: [ RUN ] FileNameOptionTest.HandlesOptionalUnsetOption
19: [ OK ] FileNameOptionTest.HandlesOptionalUnsetOption (0 ms)
19: [ RUN ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension
19: [ OK ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension (0 ms)
19: [ RUN ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension
19: [ OK ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension (0 ms)
19: [ RUN ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension
19: [ OK ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension (0 ms)
19: [ RUN ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix
19: [ OK ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix (1 ms)
19: [ RUN ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix
19: [ OK ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix (0 ms)
19: [----------] 8 tests from FileNameOptionTest (2 ms total)
19:
19: [----------] 15 tests from FileNameOptionManagerTest
19: [ RUN ] FileNameOptionManagerTest.AddsMissingExtension
19: [ OK ] FileNameOptionManagerTest.AddsMissingExtension (0 ms)
19: [ RUN ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension
19: [ OK ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension (0 ms)
19: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile
19: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile (1 ms)
19: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile
19: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile (0 ms)
19: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile
19: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile (1 ms)
19: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile
19: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile (0 ms)
19: [ RUN ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified
19: [ OK ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified (0 ms)
19: [ RUN ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified
19: [ OK ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified (1 ms)
19: [ RUN ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified
19: [ OK ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified (0 ms)
19: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile
19: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile (0 ms)
19: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile
19: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile (1 ms)
19: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile
19: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile (0 ms)
19: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile
19: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile (0 ms)
19: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile
19: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile (0 ms)
19: [ RUN ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking
19: [ OK ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking (1 ms)
19: [----------] 15 tests from FileNameOptionManagerTest (5 ms total)
19:
19: [----------] 1 test from OptionsTest
19: [ RUN ] OptionsTest.FailsOnNonsafeStorage
19: [ OK ] OptionsTest.FailsOnNonsafeStorage (0 ms)
19: [----------] 1 test from OptionsTest (0 ms total)
19:
19: [----------] 9 tests from OptionsAssignerTest
19: [ RUN ] OptionsAssignerTest.HandlesMissingRequiredParameter
19: [ OK ] OptionsAssignerTest.HandlesMissingRequiredParameter (0 ms)
19: [ RUN ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue
19: [ OK ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue (0 ms)
19: [ RUN ] OptionsAssignerTest.HandlesInvalidMultipleParameter
19: [ OK ] OptionsAssignerTest.HandlesInvalidMultipleParameter (1 ms)
19: [ RUN ] OptionsAssignerTest.HandlesMultipleParameter
19: [ OK ] OptionsAssignerTest.HandlesMultipleParameter (0 ms)
19: [ RUN ] OptionsAssignerTest.HandlesMissingValue
19: [ OK ] OptionsAssignerTest.HandlesMissingValue (0 ms)
19: [ RUN ] OptionsAssignerTest.HandlesExtraValue
19: [ OK ] OptionsAssignerTest.HandlesExtraValue (1 ms)
19: [ RUN ] OptionsAssignerTest.HandlesGroups
19: [ OK ] OptionsAssignerTest.HandlesGroups (0 ms)
19: [ RUN ] OptionsAssignerTest.HandlesSections
19: [ OK ] OptionsAssignerTest.HandlesSections (0 ms)
19: [ RUN ] OptionsAssignerTest.HandlesMultipleSources
19: [ OK ] OptionsAssignerTest.HandlesMultipleSources (0 ms)
19: [----------] 9 tests from OptionsAssignerTest (3 ms total)
19:
19: [----------] 4 tests from OptionsAssignerBooleanTest
19: [ RUN ] OptionsAssignerBooleanTest.StoresYesValue
19: [ OK ] OptionsAssignerBooleanTest.StoresYesValue (0 ms)
19: [ RUN ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue
19: [ OK ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue (0 ms)
19: [ RUN ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo
19: [ OK ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo (0 ms)
19: [ RUN ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue
19: [ OK ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue (0 ms)
19: [----------] 4 tests from OptionsAssignerBooleanTest (1 ms total)
19:
19: [----------] 13 tests from OptionsAssignerIntegerTest
19: [ RUN ] OptionsAssignerIntegerTest.StoresSingleValue
19: [ OK ] OptionsAssignerIntegerTest.StoresSingleValue (0 ms)
19: [ RUN ] OptionsAssignerIntegerTest.HandlesEmptyValue
19: [ OK ] OptionsAssignerIntegerTest.HandlesEmptyValue (0 ms)
19: [ RUN ] OptionsAssignerIntegerTest.HandlesInvalidValue
19: [ OK ] OptionsAssignerIntegerTest.HandlesInvalidValue (0 ms)
19: [ RUN ] OptionsAssignerIntegerTest.HandlesOverflow
19: [ OK ] OptionsAssignerIntegerTest.HandlesOverflow (1 ms)
19: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValue
19: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValue (0 ms)
19: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet
19: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet (0 ms)
19: [ RUN ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet
19: [ OK ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet (0 ms)
19: [ RUN ] OptionsAssignerIntegerTest.HandlesBothDefaultValues
19: [ OK ] OptionsAssignerIntegerTest.HandlesBothDefaultValues (0 ms)
19: [ RUN ] OptionsAssignerIntegerTest.StoresToVector
19: [ OK ] OptionsAssignerIntegerTest.StoresToVector (0 ms)
19: [ RUN ] OptionsAssignerIntegerTest.HandlesVectors
19: [ OK ] OptionsAssignerIntegerTest.HandlesVectors (0 ms)
19: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue
19: [ OK ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue (0 ms)
19: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue
19: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue (0 ms)
19: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment
19: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment (0 ms)
19: [----------] 13 tests from OptionsAssignerIntegerTest (3 ms total)
19:
19: [----------] 5 tests from OptionsAssignerDoubleTest
19: [ RUN ] OptionsAssignerDoubleTest.StoresSingleValue
19: [ OK ] OptionsAssignerDoubleTest.StoresSingleValue (0 ms)
19: [ RUN ] OptionsAssignerDoubleTest.StoresValueFromFloat
19: [ OK ] OptionsAssignerDoubleTest.StoresValueFromFloat (0 ms)
19: [ RUN ] OptionsAssignerDoubleTest.HandlesEmptyValue
19: [ OK ] OptionsAssignerDoubleTest.HandlesEmptyValue (0 ms)
19: [ RUN ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue
19: [ OK ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue (0 ms)
19: [ RUN ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue
19: [ OK ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue (0 ms)
19: [----------] 5 tests from OptionsAssignerDoubleTest (0 ms total)
19:
19: [----------] 9 tests from OptionsAssignerStringTest
19: [ RUN ] OptionsAssignerStringTest.StoresSingleValue
19: [ OK ] OptionsAssignerStringTest.StoresSingleValue (0 ms)
19: [ RUN ] OptionsAssignerStringTest.HandlesEnumValue
19: [ OK ] OptionsAssignerStringTest.HandlesEnumValue (0 ms)
19: [ RUN ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray
19: [ OK ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray (0 ms)
19: [ RUN ] OptionsAssignerStringTest.HandlesIncorrectEnumValue
19: [ OK ] OptionsAssignerStringTest.HandlesIncorrectEnumValue (0 ms)
19: [ RUN ] OptionsAssignerStringTest.CompletesEnumValue
19: [ OK ] OptionsAssignerStringTest.CompletesEnumValue (0 ms)
19: [ RUN ] OptionsAssignerStringTest.HandlesEnumWithNoValue
19: [ OK ] OptionsAssignerStringTest.HandlesEnumWithNoValue (0 ms)
19: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValue
19: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValue (0 ms)
19: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable
19: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable (0 ms)
19: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector
19: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector (0 ms)
19: [----------] 9 tests from OptionsAssignerStringTest (1 ms total)
19:
19: [----------] 6 tests from OptionsAssignerEnumTest
19: [ RUN ] OptionsAssignerEnumTest.StoresSingleValue
19: [ OK ] OptionsAssignerEnumTest.StoresSingleValue (0 ms)
19: [ RUN ] OptionsAssignerEnumTest.StoresVectorValues
19: [ OK ] OptionsAssignerEnumTest.StoresVectorValues (0 ms)
19: [ RUN ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange
19: [ OK ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange (0 ms)
19: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValue
19: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValue (0 ms)
19: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable
19: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable (0 ms)
19: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector
19: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector (0 ms)
19: [----------] 6 tests from OptionsAssignerEnumTest (1 ms total)
19:
19: [----------] 8 tests from RepeatingOptionSectionTest
19: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstance
19: [ OK ] RepeatingOptionSectionTest.HandlesNoInstance (0 ms)
19: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption
19: [ OK ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption (0 ms)
19: [ RUN ] RepeatingOptionSectionTest.HandlesSingleInstance
19: [ OK ] RepeatingOptionSectionTest.HandlesSingleInstance (0 ms)
19: [ RUN ] RepeatingOptionSectionTest.HandlesDefaultValue
19: [ OK ] RepeatingOptionSectionTest.HandlesDefaultValue (0 ms)
19: [ RUN ] RepeatingOptionSectionTest.HandlesTwoInstances
19: [ OK ] RepeatingOptionSectionTest.HandlesTwoInstances (0 ms)
19: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault
19: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault (0 ms)
19: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault
19: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault (1 ms)
19: [ RUN ] RepeatingOptionSectionTest.HandlesNestedSections
19: [ OK ] RepeatingOptionSectionTest.HandlesNestedSections (0 ms)
19: [----------] 8 tests from RepeatingOptionSectionTest (1 ms total)
19:
19: [----------] 1 test from TimeUnitManagerTest
19: [ RUN ] TimeUnitManagerTest.BasicOperations
19: [ OK ] TimeUnitManagerTest.BasicOperations (0 ms)
19: [----------] 1 test from TimeUnitManagerTest (0 ms total)
19:
19: [----------] 4 tests from TimeUnitBehaviorTest
19: [ RUN ] TimeUnitBehaviorTest.ScalesAssignedOptionValue
19: [ OK ] TimeUnitBehaviorTest.ScalesAssignedOptionValue (0 ms)
19: [ RUN ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues
19: [ OK ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues (0 ms)
19: [ RUN ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources
19: [ OK ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources (0 ms)
19: [ RUN ] TimeUnitBehaviorTest.TimeUnitOptionWorks
19: [ OK ] TimeUnitBehaviorTest.TimeUnitOptionWorks (0 ms)
19: [----------] 4 tests from TimeUnitBehaviorTest (0 ms total)
19:
19: [----------] 2 tests from TreeValueSupportAssignTest
19: [ RUN ] TreeValueSupportAssignTest.AssignsFromTree
19: [ OK ] TreeValueSupportAssignTest.AssignsFromTree (1 ms)
19: [ RUN ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays
19: [ OK ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays (0 ms)
19: [----------] 2 tests from TreeValueSupportAssignTest (1 ms total)
19:
19: [----------] 1 test from TreeValueSupportAssignErrorTest
19: [ RUN ] TreeValueSupportAssignErrorTest.HandlesInvalidValue
19: [ OK ] TreeValueSupportAssignErrorTest.HandlesInvalidValue (0 ms)
19: [----------] 1 test from TreeValueSupportAssignErrorTest (0 ms total)
19:
19: [----------] 5 tests from TreeValueSupportCheckTest
19: [ RUN ] TreeValueSupportCheckTest.HandlesEmpty
19: [ OK ] TreeValueSupportCheckTest.HandlesEmpty (0 ms)
19: [ RUN ] TreeValueSupportCheckTest.HandlesMatchingTree
19: [ OK ] TreeValueSupportCheckTest.HandlesMatchingTree (0 ms)
19: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree1
19: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree1 (0 ms)
19: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree2
19: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree2 (0 ms)
19: [ RUN ] TreeValueSupportCheckTest.DetectsExtraValue
19: [ OK ] TreeValueSupportCheckTest.DetectsExtraValue (0 ms)
19: [----------] 5 tests from TreeValueSupportCheckTest (1 ms total)
19:
19: [----------] 6 tests from TreeValueSupportAdjustTest
19: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultValues
19: [ OK ] TreeValueSupportAdjustTest.FillsDefaultValues (1 ms)
19: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultVectorValues
19: [ OK ] TreeValueSupportAdjustTest.FillsDefaultVectorValues (0 ms)
19: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultObjectValues
19: [ OK ] TreeValueSupportAdjustTest.FillsDefaultObjectValues (1 ms)
19: [ RUN ] TreeValueSupportAdjustTest.NormalizesValues
19: [ OK ] TreeValueSupportAdjustTest.NormalizesValues (0 ms)
19: [ RUN ] TreeValueSupportAdjustTest.MergesDefaultValues
19: [ OK ] TreeValueSupportAdjustTest.MergesDefaultValues (1 ms)
19: [ RUN ] TreeValueSupportAdjustTest.OrdersValues
19: [ OK ] TreeValueSupportAdjustTest.OrdersValues (0 ms)
19: [----------] 6 tests from TreeValueSupportAdjustTest (4 ms total)
19:
19: [----------] 8 tests from TreeValueSupportTest
19: [ RUN ] TreeValueSupportTest.SupportsBooleanOption
19: [ OK ] TreeValueSupportTest.SupportsBooleanOption (0 ms)
19: [ RUN ] TreeValueSupportTest.SupportsIntegerOption
19: [ OK ] TreeValueSupportTest.SupportsIntegerOption (1 ms)
19: [ RUN ] TreeValueSupportTest.SupportsInt64Option
19: [ OK ] TreeValueSupportTest.SupportsInt64Option (1 ms)
19: [ RUN ] TreeValueSupportTest.SupportsStringOption
19: [ OK ] TreeValueSupportTest.SupportsStringOption (1 ms)
19: [ RUN ] TreeValueSupportTest.SupportsFloatOption
19: [ OK ] TreeValueSupportTest.SupportsFloatOption (0 ms)
19: [ RUN ] TreeValueSupportTest.SupportsDoubleOption
19: [ OK ] TreeValueSupportTest.SupportsDoubleOption (1 ms)
19: [ RUN ] TreeValueSupportTest.SupportsEnumIntOption
19: [ OK ] TreeValueSupportTest.SupportsEnumIntOption (1 ms)
19: [ RUN ] TreeValueSupportTest.SupportsEnumOption
19: [ OK ] TreeValueSupportTest.SupportsEnumOption (1 ms)
19: [----------] 8 tests from TreeValueSupportTest (6 ms total)
19:
19: [----------] Global test environment tear-down
19: [==========] 110 tests from 18 test cases ran. (37 ms total)
19: [ PASSED ] 110 tests.
19/52 Test #19: OptionsUnitTests .................... Passed 0.11 sec
test 20
Start 20: PbcutilUnitTest
20: Test command: /<<PKGBUILDDIR>>/build/basic/bin/pbcutil-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/PbcutilUnitTest.xml"
20: Test timeout computed to be: 30
20: [==========] Running 3 tests from 2 test cases.
20: [----------] Global test environment set-up.
20: [----------] 1 test from PbcTest
20: [ RUN ] PbcTest.CalcShiftsWorks
20: [ OK ] PbcTest.CalcShiftsWorks (11 ms)
20: [----------] 1 test from PbcTest (12 ms total)
20:
20: [----------] 2 tests from PbcEnumsTest
20: [ RUN ] PbcEnumsTest.CenteringTypeNamesAreCorrect
20: [ OK ] PbcEnumsTest.CenteringTypeNamesAreCorrect (0 ms)
20: [ RUN ] PbcEnumsTest.UnitCellTypeNamesAreCorrect
20: [ OK ] PbcEnumsTest.UnitCellTypeNamesAreCorrect (0 ms)
20: [----------] 2 tests from PbcEnumsTest (0 ms total)
20:
20: [----------] Global test environment tear-down
20: [==========] 3 tests from 2 test cases ran. (13 ms total)
20: [ PASSED ] 3 tests.
20/52 Test #20: PbcutilUnitTest ..................... Passed 0.07 sec
test 21
Start 21: RandomUnitTests
21: Test command: /<<PKGBUILDDIR>>/build/basic/bin/random-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/RandomUnitTests.xml"
21: Test timeout computed to be: 30
21: [==========] Running 44 tests from 10 test cases.
21: [----------] Global test environment set-up.
21: [----------] 4 tests from ExponentialDistributionTest
21: [ RUN ] ExponentialDistributionTest.Output
21: [ OK ] ExponentialDistributionTest.Output (14 ms)
21: [ RUN ] ExponentialDistributionTest.Logical
21: [ OK ] ExponentialDistributionTest.Logical (0 ms)
21: [ RUN ] ExponentialDistributionTest.Reset
21: [ OK ] ExponentialDistributionTest.Reset (0 ms)
21: [ RUN ] ExponentialDistributionTest.AltParam
21: [ OK ] ExponentialDistributionTest.AltParam (0 ms)
21: [----------] 4 tests from ExponentialDistributionTest (14 ms total)
21:
21: [----------] 4 tests from GammaDistributionTest
21: [ RUN ] GammaDistributionTest.Output
21: [ OK ] GammaDistributionTest.Output (1 ms)
21: [ RUN ] GammaDistributionTest.Logical
21: [ OK ] GammaDistributionTest.Logical (0 ms)
21: [ RUN ] GammaDistributionTest.Reset
21: [ OK ] GammaDistributionTest.Reset (0 ms)
21: [ RUN ] GammaDistributionTest.AltParam
21: [ OK ] GammaDistributionTest.AltParam (0 ms)
21: [----------] 4 tests from GammaDistributionTest (1 ms total)
21:
21: [----------] 4 tests from NormalDistributionTest
21: [ RUN ] NormalDistributionTest.Output
21: [ OK ] NormalDistributionTest.Output (1 ms)
21: [ RUN ] NormalDistributionTest.Logical
21: [ OK ] NormalDistributionTest.Logical (0 ms)
21: [ RUN ] NormalDistributionTest.Reset
21: [ OK ] NormalDistributionTest.Reset (0 ms)
21: [ RUN ] NormalDistributionTest.AltParam
21: [ OK ] NormalDistributionTest.AltParam (0 ms)
21: [----------] 4 tests from NormalDistributionTest (1 ms total)
21:
21: [----------] 1 test from SeedTest
21: [ RUN ] SeedTest.makeRandomSeed
21: [ OK ] SeedTest.makeRandomSeed (13 ms)
21: [----------] 1 test from SeedTest (13 ms total)
21:
21: [----------] 6 tests from TabulatedNormalDistributionTest
21: [ RUN ] TabulatedNormalDistributionTest.Output14
21: [ OK ] TabulatedNormalDistributionTest.Output14 (1 ms)
21: [ RUN ] TabulatedNormalDistributionTest.Output16
21: [ OK ] TabulatedNormalDistributionTest.Output16 (1 ms)
21: [ RUN ] TabulatedNormalDistributionTest.OutputDouble14
21: [ OK ] TabulatedNormalDistributionTest.OutputDouble14 (1 ms)
21: [ RUN ] TabulatedNormalDistributionTest.Logical
21: [ OK ] TabulatedNormalDistributionTest.Logical (0 ms)
21: [ RUN ] TabulatedNormalDistributionTest.Reset
21: [ OK ] TabulatedNormalDistributionTest.Reset (0 ms)
21: [ RUN ] TabulatedNormalDistributionTest.AltParam
21: [ OK ] TabulatedNormalDistributionTest.AltParam (0 ms)
21: [----------] 6 tests from TabulatedNormalDistributionTest (3 ms total)
21:
21: [----------] 1 test from TabulatedNormalDistributionTableTest
21: [ RUN ] TabulatedNormalDistributionTableTest.HasValidProperties
21: [ OK ] TabulatedNormalDistributionTableTest.HasValidProperties (8 ms)
21: [----------] 1 test from TabulatedNormalDistributionTableTest (8 ms total)
21:
21: [----------] 6 tests from ThreeFry2x64Test
21: [ RUN ] ThreeFry2x64Test.Logical
21: [ OK ] ThreeFry2x64Test.Logical (0 ms)
21: [ RUN ] ThreeFry2x64Test.InternalCounterSequence
21: [ OK ] ThreeFry2x64Test.InternalCounterSequence (1 ms)
21: [ RUN ] ThreeFry2x64Test.Reseed
21: [ OK ] ThreeFry2x64Test.Reseed (0 ms)
21: [ RUN ] ThreeFry2x64Test.Discard
21: [ OK ] ThreeFry2x64Test.Discard (0 ms)
21: [ RUN ] ThreeFry2x64Test.InvalidCounter
21: [ OK ] ThreeFry2x64Test.InvalidCounter (1 ms)
21: [ RUN ] ThreeFry2x64Test.ExhaustInternalCounter
21: [ OK ] ThreeFry2x64Test.ExhaustInternalCounter (0 ms)
21: [----------] 6 tests from ThreeFry2x64Test (2 ms total)
21:
21: [----------] 4 tests from UniformIntDistributionTest
21: [ RUN ] UniformIntDistributionTest.Output
21: [ OK ] UniformIntDistributionTest.Output (1 ms)
21: [ RUN ] UniformIntDistributionTest.Logical
21: [ OK ] UniformIntDistributionTest.Logical (0 ms)
21: [ RUN ] UniformIntDistributionTest.Reset
21: [ OK ] UniformIntDistributionTest.Reset (0 ms)
21: [ RUN ] UniformIntDistributionTest.AltParam
21: [ OK ] UniformIntDistributionTest.AltParam (0 ms)
21: [----------] 4 tests from UniformIntDistributionTest (1 ms total)
21:
21: [----------] 5 tests from UniformRealDistributionTest
21: [ RUN ] UniformRealDistributionTest.GenerateCanonical
21: [ OK ] UniformRealDistributionTest.GenerateCanonical (1 ms)
21: [ RUN ] UniformRealDistributionTest.Output
21: [ OK ] UniformRealDistributionTest.Output (0 ms)
21: [ RUN ] UniformRealDistributionTest.Logical
21: [ OK ] UniformRealDistributionTest.Logical (0 ms)
21: [ RUN ] UniformRealDistributionTest.Reset
21: [ OK ] UniformRealDistributionTest.Reset (0 ms)
21: [ RUN ] UniformRealDistributionTest.AltParam
21: [ OK ] UniformRealDistributionTest.AltParam (0 ms)
21: [----------] 5 tests from UniformRealDistributionTest (1 ms total)
21:
21: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test
21: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/0
21: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/0 (1 ms)
21: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/1
21: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/1 (0 ms)
21: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/2
21: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/2 (0 ms)
21: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/0
21: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 (0 ms)
21: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/1
21: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 (0 ms)
21: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/2
21: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 (1 ms)
21: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0
21: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 (0 ms)
21: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1
21: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 (1 ms)
21: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2
21: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 (0 ms)
21: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test (5 ms total)
21:
21: [----------] Global test environment tear-down
21: [==========] 44 tests from 10 test cases ran. (51 ms total)
21: [ PASSED ] 44 tests.
21/52 Test #21: RandomUnitTests ..................... Passed 0.16 sec
test 22
Start 22: RestraintTests
22: Test command: /<<PKGBUILDDIR>>/build/basic/bin/restraintpotential-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/RestraintTests.xml"
22: Test timeout computed to be: 30
22: [==========] Running 1 test from 1 test case.
22: [----------] Global test environment set-up.
22: [----------] 1 test from RestraintManager
22: [ RUN ] RestraintManager.restraintList
22: [ OK ] RestraintManager.restraintList (0 ms)
22: [----------] 1 test from RestraintManager (1 ms total)
22:
22: [----------] Global test environment tear-down
22: [==========] 1 test from 1 test case ran. (3 ms total)
22: [ PASSED ] 1 test.
22/52 Test #22: RestraintTests ...................... Passed 0.06 sec
test 23
Start 23: TableUnitTests
23: Test command: /<<PKGBUILDDIR>>/build/basic/bin/table-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/TableUnitTests.xml"
23: Test timeout computed to be: 30
23: [==========] Running 16 tests from 2 test cases.
23: [----------] Global test environment set-up.
23: [----------] 8 tests from SplineTableTest/0, where TypeParam = gmx::QuadraticSplineTable
23: [ RUN ] SplineTableTest/0.HandlesIncorrectInput
23: [ OK ] SplineTableTest/0.HandlesIncorrectInput (7 ms)
23: [ RUN ] SplineTableTest/0.Sinc
23: [ OK ] SplineTableTest/0.Sinc (4 ms)
23: [ RUN ] SplineTableTest/0.LJ12
23: [ OK ] SplineTableTest/0.LJ12 (80 ms)
23: [ RUN ] SplineTableTest/0.PmeCorrection
23: [ OK ] SplineTableTest/0.PmeCorrection (7 ms)
23: [ RUN ] SplineTableTest/0.HandlesIncorrectNumericalInput
23: [ OK ] SplineTableTest/0.HandlesIncorrectNumericalInput (2 ms)
23: [ RUN ] SplineTableTest/0.NumericalInputPmeCorr
23: [ OK ] SplineTableTest/0.NumericalInputPmeCorr (6 ms)
23: [ RUN ] SplineTableTest/0.TwoFunctions
23: [ OK ] SplineTableTest/0.TwoFunctions (162 ms)
23: [ RUN ] SplineTableTest/0.ThreeFunctions
23: [ OK ] SplineTableTest/0.ThreeFunctions (188 ms)
23: [----------] 8 tests from SplineTableTest/0 (456 ms total)
23:
23: [----------] 8 tests from SplineTableTest/1, where TypeParam = gmx::CubicSplineTable
23: [ RUN ] SplineTableTest/1.HandlesIncorrectInput
23: [ OK ] SplineTableTest/1.HandlesIncorrectInput (6 ms)
23: [ RUN ] SplineTableTest/1.Sinc
23: [ OK ] SplineTableTest/1.Sinc (3 ms)
23: [ RUN ] SplineTableTest/1.LJ12
23: [ OK ] SplineTableTest/1.LJ12 (12 ms)
23: [ RUN ] SplineTableTest/1.PmeCorrection
23: [ OK ] SplineTableTest/1.PmeCorrection (8 ms)
23: [ RUN ] SplineTableTest/1.HandlesIncorrectNumericalInput
23: [ OK ] SplineTableTest/1.HandlesIncorrectNumericalInput (1 ms)
23: [ RUN ] SplineTableTest/1.NumericalInputPmeCorr
23: [ OK ] SplineTableTest/1.NumericalInputPmeCorr (6 ms)
23: [ RUN ] SplineTableTest/1.TwoFunctions
23: [ OK ] SplineTableTest/1.TwoFunctions (24 ms)
23: [ RUN ] SplineTableTest/1.ThreeFunctions
23: [ OK ] SplineTableTest/1.ThreeFunctions (27 ms)
23: [----------] 8 tests from SplineTableTest/1 (88 ms total)
23:
23: [----------] Global test environment tear-down
23: [==========] 16 tests from 2 test cases ran. (544 ms total)
23: [ PASSED ] 16 tests.
23/52 Test #23: TableUnitTests ...................... Passed 0.61 sec
test 24
Start 24: TaskAssignmentUnitTests
24: Test command: /<<PKGBUILDDIR>>/build/basic/bin/taskassignment-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/TaskAssignmentUnitTests.xml"
24: Test timeout computed to be: 30
24: [==========] Running 3 tests from 2 test cases.
24: [----------] Global test environment set-up.
24: [----------] 2 tests from UserTaskAssignmentStringHandlingTest
24: [ RUN ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork
24: [ OK ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork (1 ms)
24: [ RUN ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid
24: [ OK ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid (0 ms)
24: [----------] 2 tests from UserTaskAssignmentStringHandlingTest (2 ms total)
24:
24: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest
24: [ RUN ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow
24: [ OK ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow (2 ms)
24: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest (2 ms total)
24:
24: [----------] Global test environment tear-down
24: [==========] 3 tests from 2 test cases ran. (7 ms total)
24: [ PASSED ] 3 tests.
24/52 Test #24: TaskAssignmentUnitTests ............. Passed 0.07 sec
test 25
Start 25: TopologyTest
25: Test command: /<<PKGBUILDDIR>>/build/basic/bin/topology-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/TopologyTest.xml"
25: Test timeout computed to be: 30
25: [==========] Running 11 tests from 3 test cases.
25: [----------] Global test environment set-up.
25: [----------] 3 tests from ExclusionBlockTest
25: [ RUN ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks
25: [ OK ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks (1 ms)
25: [ RUN ] ExclusionBlockTest.ConvertExclusionBlockToBlocka
25: [ OK ] ExclusionBlockTest.ConvertExclusionBlockToBlocka (0 ms)
25: [ RUN ] ExclusionBlockTest.MergeExclusions
25: [ OK ] ExclusionBlockTest.MergeExclusions (0 ms)
25: [----------] 3 tests from ExclusionBlockTest (1 ms total)
25:
25: [----------] 2 tests from MtopTest
25: [ RUN ] MtopTest.RangeBasedLoop
25: [ OK ] MtopTest.RangeBasedLoop (0 ms)
25: [ RUN ] MtopTest.Operators
25: [ OK ] MtopTest.Operators (0 ms)
25: [----------] 2 tests from MtopTest (0 ms total)
25:
25: [----------] 6 tests from SymtabTest
25: [ RUN ] SymtabTest.EmptyOnOpen
25: [ OK ] SymtabTest.EmptyOnOpen (1 ms)
25: [ RUN ] SymtabTest.AddSingleEntry
25: [ OK ] SymtabTest.AddSingleEntry (0 ms)
25: [ RUN ] SymtabTest.AddTwoDistinctEntries
25: [ OK ] SymtabTest.AddTwoDistinctEntries (0 ms)
25: [ RUN ] SymtabTest.TryToAddDuplicates
25: [ OK ] SymtabTest.TryToAddDuplicates (0 ms)
25: [ RUN ] SymtabTest.AddLargeNumberOfEntries
25: [ OK ] SymtabTest.AddLargeNumberOfEntries (1 ms)
25: [ RUN ] SymtabTest.NoDuplicatesInLargeTable
25: [ OK ] SymtabTest.NoDuplicatesInLargeTable (1 ms)
25: [----------] 6 tests from SymtabTest (3 ms total)
25:
25: [----------] Global test environment tear-down
25: [==========] 11 tests from 3 test cases ran. (4 ms total)
25: [ PASSED ] 11 tests.
25/52 Test #25: TopologyTest ........................ Passed 0.07 sec
test 26
Start 26: PullTest
26: Test command: /<<PKGBUILDDIR>>/build/basic/bin/pull-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/PullTest.xml"
26: Test timeout computed to be: 30
26: [==========] Running 5 tests from 1 test case.
26: [----------] Global test environment set-up.
26: [----------] 5 tests from PullTest
26: [ RUN ] PullTest.MaxPullDistanceXyzScrewBox
26: [ OK ] PullTest.MaxPullDistanceXyzScrewBox (0 ms)
26: [ RUN ] PullTest.MaxPullDistanceXyzCubicBox
26: [ OK ] PullTest.MaxPullDistanceXyzCubicBox (0 ms)
26: [ RUN ] PullTest.MaxPullDistanceXyzTricBox
26: [ OK ] PullTest.MaxPullDistanceXyzTricBox (0 ms)
26: [ RUN ] PullTest.MaxPullDistanceXyzLongBox
26: [ OK ] PullTest.MaxPullDistanceXyzLongBox (0 ms)
26: [ RUN ] PullTest.MaxPullDistanceXySkewedBox
26: [ OK ] PullTest.MaxPullDistanceXySkewedBox (0 ms)
26: [----------] 5 tests from PullTest (2 ms total)
26:
26: [----------] Global test environment tear-down
26: [==========] 5 tests from 1 test case ran. (4 ms total)
26: [ PASSED ] 5 tests.
26/52 Test #26: PullTest ............................ Passed 0.07 sec
test 27
Start 27: AwhTest
27: Test command: /<<PKGBUILDDIR>>/build/basic/bin/awh-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/AwhTest.xml"
27: Test timeout computed to be: 30
27: [==========] Running 12 tests from 4 test cases.
27: [----------] Global test environment set-up.
27: [----------] 1 test from BiasTest
27: [ RUN ] BiasTest.DetectsCovering
27: [ OK ] BiasTest.DetectsCovering (3 ms)
27: [----------] 1 test from BiasTest (3 ms total)
27:
27: [----------] 1 test from gridTest
27: [ RUN ] gridTest.neighborhood
27: [ OK ] gridTest.neighborhood (9 ms)
27: [----------] 1 test from gridTest (9 ms total)
27:
27: [----------] 8 tests from WithParameters/BiasTest
27: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/0
27: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/0 (16 ms)
27: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/1
27: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/1 (3 ms)
27: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/2
27: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/2 (2 ms)
27: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/3
27: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/3 (3 ms)
27: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/4
27: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/4 (3 ms)
27: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/5
27: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/5 (2 ms)
27: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/6
27: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/6 (3 ms)
27: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/7
27: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/7 (3 ms)
27: [----------] 8 tests from WithParameters/BiasTest (40 ms total)
27:
27: [----------] 2 tests from WithParameters/BiasStateTest
27: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/0
27: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/0 (2 ms)
27: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/1
27: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/1 (18 ms)
27: [----------] 2 tests from WithParameters/BiasStateTest (21 ms total)
27:
27: [----------] Global test environment tear-down
27: [==========] 12 tests from 4 test cases ran. (78 ms total)
27: [ PASSED ] 12 tests.
27/52 Test #27: AwhTest ............................. Passed 0.14 sec
test 28
Start 28: SimdUnitTests
28: Test command: /<<PKGBUILDDIR>>/build/basic/bin/simd-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/SimdUnitTests.xml"
28: Test timeout computed to be: 30
28: [==========] Running 86 tests from 3 test cases.
28: [----------] Global test environment set-up.
28: [----------] 41 tests from SimdScalarTest
28: [ RUN ] SimdScalarTest.load
28: [ OK ] SimdScalarTest.load (0 ms)
28: [ RUN ] SimdScalarTest.loadU
28: [ OK ] SimdScalarTest.loadU (0 ms)
28: [ RUN ] SimdScalarTest.store
28: [ OK ] SimdScalarTest.store (0 ms)
28: [ RUN ] SimdScalarTest.storeU
28: [ OK ] SimdScalarTest.storeU (0 ms)
28: [ RUN ] SimdScalarTest.setZero
28: [ OK ] SimdScalarTest.setZero (0 ms)
28: [ RUN ] SimdScalarTest.andNot
28: [ OK ] SimdScalarTest.andNot (0 ms)
28: [ RUN ] SimdScalarTest.fma
28: [ OK ] SimdScalarTest.fma (0 ms)
28: [ RUN ] SimdScalarTest.fms
28: [ OK ] SimdScalarTest.fms (0 ms)
28: [ RUN ] SimdScalarTest.fnma
28: [ OK ] SimdScalarTest.fnma (0 ms)
28: [ RUN ] SimdScalarTest.fnms
28: [ OK ] SimdScalarTest.fnms (0 ms)
28: [ RUN ] SimdScalarTest.maskAdd
28: [ OK ] SimdScalarTest.maskAdd (0 ms)
28: [ RUN ] SimdScalarTest.maskzMul
28: [ OK ] SimdScalarTest.maskzMul (0 ms)
28: [ RUN ] SimdScalarTest.maskzFma
28: [ OK ] SimdScalarTest.maskzFma (0 ms)
28: [ RUN ] SimdScalarTest.abs
28: [ OK ] SimdScalarTest.abs (0 ms)
28: [ RUN ] SimdScalarTest.max
28: [ OK ] SimdScalarTest.max (0 ms)
28: [ RUN ] SimdScalarTest.min
28: [ OK ] SimdScalarTest.min (0 ms)
28: [ RUN ] SimdScalarTest.round
28: [ OK ] SimdScalarTest.round (0 ms)
28: [ RUN ] SimdScalarTest.trunc
28: [ OK ] SimdScalarTest.trunc (0 ms)
28: [ RUN ] SimdScalarTest.reduce
28: [ OK ] SimdScalarTest.reduce (0 ms)
28: [ RUN ] SimdScalarTest.testBits
28: [ OK ] SimdScalarTest.testBits (0 ms)
28: [ RUN ] SimdScalarTest.anyTrue
28: [ OK ] SimdScalarTest.anyTrue (0 ms)
28: [ RUN ] SimdScalarTest.selectByMask
28: [ OK ] SimdScalarTest.selectByMask (0 ms)
28: [ RUN ] SimdScalarTest.selectByNotMask
28: [ OK ] SimdScalarTest.selectByNotMask (0 ms)
28: [ RUN ] SimdScalarTest.blend
28: [ OK ] SimdScalarTest.blend (1 ms)
28: [ RUN ] SimdScalarTest.cvtR2I
28: [ OK ] SimdScalarTest.cvtR2I (0 ms)
28: [ RUN ] SimdScalarTest.cvttR2I
28: [ OK ] SimdScalarTest.cvttR2I (0 ms)
28: [ RUN ] SimdScalarTest.cvtI2R
28: [ OK ] SimdScalarTest.cvtI2R (0 ms)
28: [ RUN ] SimdScalarTest.cvtF2D
28: [ OK ] SimdScalarTest.cvtF2D (0 ms)
28: [ RUN ] SimdScalarTest.cvtD2D
28: [ OK ] SimdScalarTest.cvtD2D (0 ms)
28: [ RUN ] SimdScalarTest.loadI
28: [ OK ] SimdScalarTest.loadI (0 ms)
28: [ RUN ] SimdScalarTest.loadUI
28: [ OK ] SimdScalarTest.loadUI (0 ms)
28: [ RUN ] SimdScalarTest.storeI
28: [ OK ] SimdScalarTest.storeI (0 ms)
28: [ RUN ] SimdScalarTest.storeUI
28: [ OK ] SimdScalarTest.storeUI (0 ms)
28: [ RUN ] SimdScalarTest.andNotI
28: [ OK ] SimdScalarTest.andNotI (0 ms)
28: [ RUN ] SimdScalarTest.testBitsI
28: [ OK ] SimdScalarTest.testBitsI (0 ms)
28: [ RUN ] SimdScalarTest.selectByMaskI
28: [ OK ] SimdScalarTest.selectByMaskI (0 ms)
28: [ RUN ] SimdScalarTest.selectByNotMaskI
28: [ OK ] SimdScalarTest.selectByNotMaskI (0 ms)
28: [ RUN ] SimdScalarTest.blendI
28: [ OK ] SimdScalarTest.blendI (0 ms)
28: [ RUN ] SimdScalarTest.cvtB2IB
28: [ OK ] SimdScalarTest.cvtB2IB (0 ms)
28: [ RUN ] SimdScalarTest.cvtIB2B
28: [ OK ] SimdScalarTest.cvtIB2B (0 ms)
28: [ RUN ] SimdScalarTest.expandScalarsToTriplets
28: [ OK ] SimdScalarTest.expandScalarsToTriplets (0 ms)
28: [----------] 41 tests from SimdScalarTest (2 ms total)
28:
28: [----------] 8 tests from SimdScalarUtilTest
28: [ RUN ] SimdScalarUtilTest.gatherLoadTranspose
28: [ OK ] SimdScalarUtilTest.gatherLoadTranspose (0 ms)
28: [ RUN ] SimdScalarUtilTest.gatherLoadUTranspose
28: [ OK ] SimdScalarUtilTest.gatherLoadUTranspose (0 ms)
28: [ RUN ] SimdScalarUtilTest.transposeScatterStoreU
28: [ OK ] SimdScalarUtilTest.transposeScatterStoreU (0 ms)
28: [ RUN ] SimdScalarUtilTest.transposeScatterIncrU
28: [ OK ] SimdScalarUtilTest.transposeScatterIncrU (0 ms)
28: [ RUN ] SimdScalarUtilTest.transposeScatterDecrU
28: [ OK ] SimdScalarUtilTest.transposeScatterDecrU (1 ms)
28: [ RUN ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose
28: [ OK ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose (0 ms)
28: [ RUN ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose
28: [ OK ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose (0 ms)
28: [ RUN ] SimdScalarUtilTest.reduceIncr4ReturnSum
28: [ OK ] SimdScalarUtilTest.reduceIncr4ReturnSum (0 ms)
28: [----------] 8 tests from SimdScalarUtilTest (1 ms total)
28:
28: [----------] 37 tests from SimdScalarMathTest
28: [ RUN ] SimdScalarMathTest.copysign
28: [ OK ] SimdScalarMathTest.copysign (0 ms)
28: [ RUN ] SimdScalarMathTest.invsqrtPair
28: [ OK ] SimdScalarMathTest.invsqrtPair (0 ms)
28: [ RUN ] SimdScalarMathTest.inv
28: [ OK ] SimdScalarMathTest.inv (0 ms)
28: [ RUN ] SimdScalarMathTest.maskzInvsqrt
28: [ OK ] SimdScalarMathTest.maskzInvsqrt (0 ms)
28: [ RUN ] SimdScalarMathTest.log
28: [ OK ] SimdScalarMathTest.log (0 ms)
28: [ RUN ] SimdScalarMathTest.exp2
28: [ OK ] SimdScalarMathTest.exp2 (0 ms)
28: [ RUN ] SimdScalarMathTest.exp
28: [ OK ] SimdScalarMathTest.exp (0 ms)
28: [ RUN ] SimdScalarMathTest.erf
28: [ OK ] SimdScalarMathTest.erf (0 ms)
28: [ RUN ] SimdScalarMathTest.erfc
28: [ OK ] SimdScalarMathTest.erfc (0 ms)
28: [ RUN ] SimdScalarMathTest.sincos
28: [ OK ] SimdScalarMathTest.sincos (0 ms)
28: [ RUN ] SimdScalarMathTest.sin
28: [ OK ] SimdScalarMathTest.sin (0 ms)
28: [ RUN ] SimdScalarMathTest.cos
28: [ OK ] SimdScalarMathTest.cos (0 ms)
28: [ RUN ] SimdScalarMathTest.tan
28: [ OK ] SimdScalarMathTest.tan (0 ms)
28: [ RUN ] SimdScalarMathTest.asin
28: [ OK ] SimdScalarMathTest.asin (0 ms)
28: [ RUN ] SimdScalarMathTest.acos
28: [ OK ] SimdScalarMathTest.acos (0 ms)
28: [ RUN ] SimdScalarMathTest.atan
28: [ OK ] SimdScalarMathTest.atan (0 ms)
28: [ RUN ] SimdScalarMathTest.atan2
28: [ OK ] SimdScalarMathTest.atan2 (0 ms)
28: [ RUN ] SimdScalarMathTest.pmeForceCorrection
28: [ OK ] SimdScalarMathTest.pmeForceCorrection (0 ms)
28: [ RUN ] SimdScalarMathTest.pmePotentialCorrection
28: [ OK ] SimdScalarMathTest.pmePotentialCorrection (0 ms)
28: [ RUN ] SimdScalarMathTest.invsqrtPairSingleAccuracy
28: [ OK ] SimdScalarMathTest.invsqrtPairSingleAccuracy (0 ms)
28: [ RUN ] SimdScalarMathTest.invSingleAccuracy
28: [ OK ] SimdScalarMathTest.invSingleAccuracy (0 ms)
28: [ RUN ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy
28: [ OK ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy (0 ms)
28: [ RUN ] SimdScalarMathTest.logSingleAccuracy
28: [ OK ] SimdScalarMathTest.logSingleAccuracy (0 ms)
28: [ RUN ] SimdScalarMathTest.exp2SingleAccuracy
28: [ OK ] SimdScalarMathTest.exp2SingleAccuracy (0 ms)
28: [ RUN ] SimdScalarMathTest.expSingleAccuracy
28: [ OK ] SimdScalarMathTest.expSingleAccuracy (0 ms)
28: [ RUN ] SimdScalarMathTest.erfSingleAccuracy
28: [ OK ] SimdScalarMathTest.erfSingleAccuracy (0 ms)
28: [ RUN ] SimdScalarMathTest.erfcSingleAccuracy
28: [ OK ] SimdScalarMathTest.erfcSingleAccuracy (0 ms)
28: [ RUN ] SimdScalarMathTest.sincosSingleAccuracy
28: [ OK ] SimdScalarMathTest.sincosSingleAccuracy (0 ms)
28: [ RUN ] SimdScalarMathTest.sinSingleAccuracy
28: [ OK ] SimdScalarMathTest.sinSingleAccuracy (0 ms)
28: [ RUN ] SimdScalarMathTest.cosSingleAccuracy
28: [ OK ] SimdScalarMathTest.cosSingleAccuracy (0 ms)
28: [ RUN ] SimdScalarMathTest.tanSingleAccuracy
28: [ OK ] SimdScalarMathTest.tanSingleAccuracy (0 ms)
28: [ RUN ] SimdScalarMathTest.asinSingleAccuracy
28: [ OK ] SimdScalarMathTest.asinSingleAccuracy (0 ms)
28: [ RUN ] SimdScalarMathTest.acosSingleAccuracy
28: [ OK ] SimdScalarMathTest.acosSingleAccuracy (0 ms)
28: [ RUN ] SimdScalarMathTest.atanSingleAccuracy
28: [ OK ] SimdScalarMathTest.atanSingleAccuracy (0 ms)
28: [ RUN ] SimdScalarMathTest.atan2SingleAccuracy
28: [ OK ] SimdScalarMathTest.atan2SingleAccuracy (0 ms)
28: [ RUN ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy
28: [ OK ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy (0 ms)
28: [ RUN ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy
28: [ OK ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy (0 ms)
28: [----------] 37 tests from SimdScalarMathTest (1 ms total)
28:
28: [----------] Global test environment tear-down
28: [==========] 86 tests from 3 test cases ran. (4 ms total)
28: [ PASSED ] 86 tests.
28/52 Test #28: SimdUnitTests ....................... Passed 0.07 sec
test 29
Start 29: CompatibilityHelpersTests
29: Test command: /<<PKGBUILDDIR>>/build/basic/bin/compat-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/CompatibilityHelpersTests.xml"
29: Test timeout computed to be: 30
29: [==========] Running 170 tests from 12 test cases.
29: [----------] Global test environment set-up.
29: [----------] 45 tests from OptionalTest
29: [ RUN ] OptionalTest.UnionCanContainNonPodTypes
29: [ OK ] OptionalTest.UnionCanContainNonPodTypes (0 ms)
29: [ RUN ] OptionalTest.CanDefaultConstructEmpty
29: [ OK ] OptionalTest.CanDefaultConstructEmpty (0 ms)
29: [ RUN ] OptionalTest.CanConstructFromNullopt
29: [ OK ] OptionalTest.CanConstructFromNullopt (0 ms)
29: [ RUN ] OptionalTest.CanDefaultConstructUsingNonDefaultConstructibleType
29: [ OK ] OptionalTest.CanDefaultConstructUsingNonDefaultConstructibleType (0 ms)
29: [ RUN ] OptionalTest.CanCopyConstructFromEmptyOptional
29: [ OK ] OptionalTest.CanCopyConstructFromEmptyOptional (0 ms)
29: [ RUN ] OptionalTest.CanMoveConstructFromEmptyOptional
29: [ OK ] OptionalTest.CanMoveConstructFromEmptyOptional (0 ms)
29: [ RUN ] OptionalTest.CanCopyConstructFromEmptyOptionalWithExplicitConversion
29: [ OK ] OptionalTest.CanCopyConstructFromEmptyOptionalWithExplicitConversion (0 ms)
29: [ RUN ] OptionalTest.CanCopyConstructFromEmptyOptionalNonExplicitConverting
29: [ OK ] OptionalTest.CanCopyConstructFromEmptyOptionalNonExplicitConverting (0 ms)
29: [ RUN ] OptionalTest.CanMoveConstructFromEmptyOptionalExplicitConverting
29: [ OK ] OptionalTest.CanMoveConstructFromEmptyOptionalExplicitConverting (0 ms)
29: [ RUN ] OptionalTest.CanMoveConstructFromEmptyOptionalNonExplicitConverting
29: [ OK ] OptionalTest.CanMoveConstructFromEmptyOptionalNonExplicitConverting (1 ms)
29: [ RUN ] OptionalTest.CanCopyConstructFromNonEmptyOptional
29: [ OK ] OptionalTest.CanCopyConstructFromNonEmptyOptional (0 ms)
29: [ RUN ] OptionalTest.CanCopyConstructFromNonEmptyOptionalExplicitConverting
29: [ OK ] OptionalTest.CanCopyConstructFromNonEmptyOptionalExplicitConverting (0 ms)
29: [ RUN ] OptionalTest.CanCopyConstructFromNonEmptyOptionalNonExplicitConverting
29: [ OK ] OptionalTest.CanCopyConstructFromNonEmptyOptionalNonExplicitConverting (0 ms)
29: [ RUN ] OptionalTest.CanMoveConstructFromNonEmptyOptional
29: [ OK ] OptionalTest.CanMoveConstructFromNonEmptyOptional (0 ms)
29: [ RUN ] OptionalTest.CanMoveConstructFromNonEmptyOptionalExplicitConverting
29: [ OK ] OptionalTest.CanMoveConstructFromNonEmptyOptionalExplicitConverting (0 ms)
29: [ RUN ] OptionalTest.CanMoveConstructFromNonEmptyOptionalNonExplicitConverting
29: [ OK ] OptionalTest.CanMoveConstructFromNonEmptyOptionalNonExplicitConverting (0 ms)
29: [ RUN ] OptionalTest.CanCopyConstructFromLiteral
29: [ OK ] OptionalTest.CanCopyConstructFromLiteral (0 ms)
29: [ RUN ] OptionalTest.CanCopyConstructFromLiteralConverting
29: [ OK ] OptionalTest.CanCopyConstructFromLiteralConverting (0 ms)
29: [ RUN ] OptionalTest.CanCopyConstructFromValue
29: [ OK ] OptionalTest.CanCopyConstructFromValue (0 ms)
29: [ RUN ] OptionalTest.CanCopyConstructFromValueConverting
29: [ OK ] OptionalTest.CanCopyConstructFromValueConverting (0 ms)
29: [ RUN ] OptionalTest.CanMoveConstructFromValue
29: [ OK ] OptionalTest.CanMoveConstructFromValue (0 ms)
29: [ RUN ] OptionalTest.CanMoveConstructFromValueExplicitConverting
29: [ OK ] OptionalTest.CanMoveConstructFromValueExplicitConverting (0 ms)
29: [ RUN ] OptionalTest.CanMoveConstructFromValueNonExplicitConverting
29: [ OK ] OptionalTest.CanMoveConstructFromValueNonExplicitConverting (0 ms)
29: [ RUN ] OptionalTest.CanInPlaceConstructFromLiteral
29: [ OK ] OptionalTest.CanInPlaceConstructFromLiteral (0 ms)
29: [ RUN ] OptionalTest.CanInPlaceCopyConstructFromValue
29: [ OK ] OptionalTest.CanInPlaceCopyConstructFromValue (0 ms)
29: [ RUN ] OptionalTest.CanInPlaceMoveConstructFromValue
29: [ OK ] OptionalTest.CanInPlaceMoveConstructFromValue (0 ms)
29: [ RUN ] OptionalTest.CanInPlaceCopyConstructFromInitializerList
29: [ OK ] OptionalTest.CanInPlaceCopyConstructFromInitializerList (0 ms)
29: [ RUN ] OptionalTest.CanInPlaceMoveConstructFromInitializerList
29: [ OK ] OptionalTest.CanInPlaceMoveConstructFromInitializerList (0 ms)
29: [ RUN ] OptionalTest.CanAssignNulloptToDisengage
29: [ OK ] OptionalTest.CanAssignNulloptToDisengage (0 ms)
29: [ RUN ] OptionalTest.CanCopyAssignBetweenEngagedAndDisengagedOptionals
29: [ OK ] OptionalTest.CanCopyAssignBetweenEngagedAndDisengagedOptionals (0 ms)
29: [ RUN ] OptionalTest.CanCopyAssignBetweenEngagedAndDisengagedOptionalsConverting
29: [ OK ] OptionalTest.CanCopyAssignBetweenEngagedAndDisengagedOptionalsConverting (0 ms)
29: [ RUN ] OptionalTest.CanMoveAssignBetweenEngagedAndDisengagedOptionalsConverting
29: [ OK ] OptionalTest.CanMoveAssignBetweenEngagedAndDisengagedOptionalsConverting (0 ms)
29: [ RUN ] OptionalTest.CanCopyAssignFromLiteral
29: [ OK ] OptionalTest.CanCopyAssignFromLiteral (0 ms)
29: [ RUN ] OptionalTest.CanCopyAssignFromValue
29: [ OK ] OptionalTest.CanCopyAssignFromValue (0 ms)
29: [ RUN ] OptionalTest.CanMoveAssignFromValue
29: [ OK ] OptionalTest.CanMoveAssignFromValue (0 ms)
29: [ RUN ] OptionalTest.CanCopyEmplaceFromArguments
29: [ OK ] OptionalTest.CanCopyEmplaceFromArguments (0 ms)
29: [ RUN ] OptionalTest.CanMoveEmplaceFromArguments
29: [ OK ] OptionalTest.CanMoveEmplaceFromArguments (0 ms)
29: [ RUN ] OptionalTest.CanCopyEmplaceFromInitializerListAndArguments
29: [ OK ] OptionalTest.CanCopyEmplaceFromInitializerListAndArguments (0 ms)
29: [ RUN ] OptionalTest.CanMoveEmplaceFromInitializerListAndArguments
29: [ OK ] OptionalTest.CanMoveEmplaceFromInitializerListAndArguments (0 ms)
29: [ RUN ] OptionalTest.CanResetContent
29: [ OK ] OptionalTest.CanResetContent (0 ms)
29: [ RUN ] OptionalTest.ProvidesRelationalOperators
29: [ OK ] OptionalTest.ProvidesRelationalOperators (1 ms)
29: [ RUN ] OptionalTest.ProvidesMixedTypeRelationalOperators
29: [ OK ] OptionalTest.ProvidesMixedTypeRelationalOperators (0 ms)
29: [ RUN ] OptionalTest.CanProduceHash
29: [ OK ] OptionalTest.CanProduceHash (0 ms)
29: [ RUN ] OptionalTest.ShowAlignmentDependingOnBaseType
29: alignment_of<char>: 1
29: alignment_of<short>: 2
29: alignment_of<int>: 4
29: alignment_of<long>: 4
29: alignment_of<float>: 4
29: alignment_of<double>: 8
29: alignment_of<long double>: 8
29: alignment_of<Struct>: 1
29: [ OK ] OptionalTest.ShowAlignmentDependingOnBaseType (0 ms)
29: [ RUN ] OptionalTest.ShowSizeDependingOnBaseType
29: sizeof( nonstd::optional_lite::detail::storage_t<char> ): 1
29: sizeof( optional<char> ): 2 (1)
29: sizeof( optional<short> ): 4 (2)
29: sizeof( optional<int> ): 8 (4)
29: sizeof( optional<long> ): 8 (4)
29: sizeof( optional<float> ): 8 (4)
29: sizeof( optional<double> ): 16 (8)
29: sizeof( optional<long double> ): 16 (8)
29: sizeof( optional<Struct> ): 2 (1)
29: [ OK ] OptionalTest.ShowSizeDependingOnBaseType (0 ms)
29: [----------] 45 tests from OptionalTest (4 ms total)
29:
29: [----------] 7 tests from MakeOptionalTest
29: [ RUN ] MakeOptionalTest.CanMoveAssignBetweenEngagedAndDisengagedOptionals
29: [ OK ] MakeOptionalTest.CanMoveAssignBetweenEngagedAndDisengagedOptionals (1 ms)
29: [ RUN ] MakeOptionalTest.CanCopyConstruct
29: [ OK ] MakeOptionalTest.CanCopyConstruct (0 ms)
29: [ RUN ] MakeOptionalTest.CanMoveConstruct
29: [ OK ] MakeOptionalTest.CanMoveConstruct (0 ms)
29: [ RUN ] MakeOptionalTest.CanInPlaceCopyConstructFromArguments
29: [ OK ] MakeOptionalTest.CanInPlaceCopyConstructFromArguments (0 ms)
29: [ RUN ] MakeOptionalTest.CanInPlaceMoveConstructFromArguments
29: [ OK ] MakeOptionalTest.CanInPlaceMoveConstructFromArguments (0 ms)
29: [ RUN ] MakeOptionalTest.CanInPlaceCopyConstructFromInitializerListAndArguments
29: [ OK ] MakeOptionalTest.CanInPlaceCopyConstructFromInitializerListAndArguments (0 ms)
29: [ RUN ] MakeOptionalTest.CanInPlaceMoveConstructFromInitializerListAndArguments
29: [ OK ] MakeOptionalTest.CanInPlaceMoveConstructFromInitializerListAndArguments (0 ms)
29: [----------] 7 tests from MakeOptionalTest (1 ms total)
29:
29: [----------] 4 tests from OptionalMemberSwapTest
29: [ RUN ] OptionalMemberSwapTest.CanSwapDisengagedWithDisengaged
29: [ OK ] OptionalMemberSwapTest.CanSwapDisengagedWithDisengaged (0 ms)
29: [ RUN ] OptionalMemberSwapTest.CanSwapEngagedWithDisengaged
29: [ OK ] OptionalMemberSwapTest.CanSwapEngagedWithDisengaged (0 ms)
29: [ RUN ] OptionalMemberSwapTest.CanSwapDisengagedWithEngaged
29: [ OK ] OptionalMemberSwapTest.CanSwapDisengagedWithEngaged (0 ms)
29: [ RUN ] OptionalMemberSwapTest.CanSwapEngagedWithEngaged
29: [ OK ] OptionalMemberSwapTest.CanSwapEngagedWithEngaged (0 ms)
29: [----------] 4 tests from OptionalMemberSwapTest (0 ms total)
29:
29: [----------] 4 tests from OptionalImplicitValueTest
29: [ RUN ] OptionalImplicitValueTest.CanObtainValueConst
29: [ OK ] OptionalImplicitValueTest.CanObtainValueConst (0 ms)
29: [ RUN ] OptionalImplicitValueTest.CanObtainValueNonConst
29: [ OK ] OptionalImplicitValueTest.CanObtainValueNonConst (0 ms)
29: [ RUN ] OptionalImplicitValueTest.CanObtainMovedFromValueConst
29: [ OK ] OptionalImplicitValueTest.CanObtainMovedFromValueConst (1 ms)
29: [ RUN ] OptionalImplicitValueTest.CanObtainMovedFromValueNonConst
29: [ OK ] OptionalImplicitValueTest.CanObtainMovedFromValueNonConst (0 ms)
29: [----------] 4 tests from OptionalImplicitValueTest (1 ms total)
29:
29: [----------] 20 tests from OptionalIntValueTest
29: [ RUN ] OptionalIntValueTest.CanObtainValueFromDereferenceOperatorConst
29: [ OK ] OptionalIntValueTest.CanObtainValueFromDereferenceOperatorConst (0 ms)
29: [ RUN ] OptionalIntValueTest.CanObtainValueFromDereferenceOperatorNonConst
29: [ OK ] OptionalIntValueTest.CanObtainValueFromDereferenceOperatorNonConst (0 ms)
29: [ RUN ] OptionalIntValueTest.CanObtainMovedValueFromDereferenceOperatorConst
29: [ OK ] OptionalIntValueTest.CanObtainMovedValueFromDereferenceOperatorConst (0 ms)
29: [ RUN ] OptionalIntValueTest.CanObtainMovedValueFromDereferenceOperatorNonConst
29: [ OK ] OptionalIntValueTest.CanObtainMovedValueFromDereferenceOperatorNonConst (0 ms)
29: [ RUN ] OptionalIntValueTest.CanObtainHasValueViaOperatorBool
29: [ OK ] OptionalIntValueTest.CanObtainHasValueViaOperatorBool (0 ms)
29: [ RUN ] OptionalIntValueTest.CanObtainValueViaValueMethodConst
29: [ OK ] OptionalIntValueTest.CanObtainValueViaValueMethodConst (0 ms)
29: [ RUN ] OptionalIntValueTest.CanObtainValueViaValueMethodNonConst
29: [ OK ] OptionalIntValueTest.CanObtainValueViaValueMethodNonConst (0 ms)
29: [ RUN ] OptionalIntValueTest.CanObtainMovedValueViaValueMethodConst
29: [ OK ] OptionalIntValueTest.CanObtainMovedValueViaValueMethodConst (0 ms)
29: [ RUN ] OptionalIntValueTest.CanObtainMovedValueViaValueMethodNonConst
29: [ OK ] OptionalIntValueTest.CanObtainMovedValueViaValueMethodNonConst (0 ms)
29: [ RUN ] OptionalIntValueTest.CanObtainValueFromNonEmptyOptionalViaValueOrMethod
29: [ OK ] OptionalIntValueTest.CanObtainValueFromNonEmptyOptionalViaValueOrMethod (0 ms)
29: [ RUN ] OptionalIntValueTest.CanObtainDefaultFromEmptyOptionalViaValueOrMethod
29: [ OK ] OptionalIntValueTest.CanObtainDefaultFromEmptyOptionalViaValueOrMethod (0 ms)
29: [ RUN ] OptionalIntValueTest.CanObtainMovedFromValueForLValuesViaValueOrMethod
29: [ OK ] OptionalIntValueTest.CanObtainMovedFromValueForLValuesViaValueOrMethod (0 ms)
29: [ RUN ] OptionalIntValueTest.CanObtainMovedFromValueForRValuesViaValueOrMethod
29: [ OK ] OptionalIntValueTest.CanObtainMovedFromValueForRValuesViaValueOrMethod (1 ms)
29: [ RUN ] OptionalIntValueTest.ThrowsBadOptionalAccessAtDisengagedAccessForLValues
29: [ OK ] OptionalIntValueTest.ThrowsBadOptionalAccessAtDisengagedAccessForLValues (0 ms)
29: [ RUN ] OptionalIntValueTest.ThrowsBadOptionalAccessAtDisengagedAccessForRValues
29: [ OK ] OptionalIntValueTest.ThrowsBadOptionalAccessAtDisengagedAccessForRValues (0 ms)
29: [ RUN ] OptionalIntValueTest.ThrowsBadOptionalAccessWithNonEmptyWhatMethod
29: [ OK ] OptionalIntValueTest.ThrowsBadOptionalAccessWithNonEmptyWhatMethod (0 ms)
29: [ RUN ] OptionalIntValueTest.CanNonMemberSwapDisengagnedWithDisengaged
29: [ OK ] OptionalIntValueTest.CanNonMemberSwapDisengagnedWithDisengaged (0 ms)
29: [ RUN ] OptionalIntValueTest.CanNonMemberSwapEngagnedWithEngaged
29: [ OK ] OptionalIntValueTest.CanNonMemberSwapEngagnedWithEngaged (0 ms)
29: [ RUN ] OptionalIntValueTest.CanNonMemberSwapDisengagnedWithEngaged
29: [ OK ] OptionalIntValueTest.CanNonMemberSwapDisengagnedWithEngaged (0 ms)
29: [ RUN ] OptionalIntValueTest.CanNonMemberSwapEngagnedWithDisengaged
29: [ OK ] OptionalIntValueTest.CanNonMemberSwapEngagnedWithDisengaged (0 ms)
29: [----------] 20 tests from OptionalIntValueTest (2 ms total)
29:
29: [----------] 1 test from NotNullConstruction
29: [ RUN ] NotNullConstruction.Works
29: [ OK ] NotNullConstruction.Works (0 ms)
29: [----------] 1 test from NotNullConstruction (0 ms total)
29:
29: [----------] 1 test from NotNullCasting
29: [ RUN ] NotNullCasting.Works
29: [ OK ] NotNullCasting.Works (0 ms)
29: [----------] 1 test from NotNullCasting (0 ms total)
29:
29: [----------] 1 test from NotNullAssignment
29: [ RUN ] NotNullAssignment.Works
29: [ OK ] NotNullAssignment.Works (0 ms)
29: [----------] 1 test from NotNullAssignment (0 ms total)
29:
29: [----------] 1 test from MakeNotNull
29: [ RUN ] MakeNotNull.Works
29: [ OK ] MakeNotNull.Works (0 ms)
29: [----------] 1 test from MakeNotNull (0 ms total)
29:
29: [----------] 1 test from NotNull
29: [ RUN ] NotNull.WorksInContainers
29: [ OK ] NotNull.WorksInContainers (0 ms)
29: [----------] 1 test from NotNull (0 ms total)
29:
29: [----------] 80 tests from StringViewTest
29: [ RUN ] StringViewTest.CanDefaultConstructEmptyView
29: [ OK ] StringViewTest.CanDefaultConstructEmptyView (0 ms)
29: [ RUN ] StringViewTest.CanConstructFromPointerAndSize
29: [ OK ] StringViewTest.CanConstructFromPointerAndSize (0 ms)
29: [ RUN ] StringViewTest.CanConstructFromCString
29: [ OK ] StringViewTest.CanConstructFromCString (0 ms)
29: [ RUN ] StringViewTest.CanCopyConstructFromEmptyView
29: [ OK ] StringViewTest.CanCopyConstructFromEmptyView (0 ms)
29: [ RUN ] StringViewTest.CanCopyConstructFromNonEmptyView
29: [ OK ] StringViewTest.CanCopyConstructFromNonEmptyView (1 ms)
29: [ RUN ] StringViewTest.CanCopyAssingFromEmptyView
29: [ OK ] StringViewTest.CanCopyAssingFromEmptyView (0 ms)
29: [ RUN ] StringViewTest.CanCopyAssingFromNonEmptyView
29: [ OK ] StringViewTest.CanCopyAssingFromNonEmptyView (0 ms)
29: [ RUN ] StringViewTest.AllowForwardIteration
29: [ OK ] StringViewTest.AllowForwardIteration (0 ms)
29: [ RUN ] StringViewTest.AllowConstForwardIteration
29: [ OK ] StringViewTest.AllowConstForwardIteration (0 ms)
29: [ RUN ] StringViewTest.AllowReverseIteration
29: [ OK ] StringViewTest.AllowReverseIteration (0 ms)
29: [ RUN ] StringViewTest.AllowConstReverseIteration
29: [ OK ] StringViewTest.AllowConstReverseIteration (0 ms)
29: [ RUN ] StringViewTest.CanObtainSizeFromViewViaSize
29: [ OK ] StringViewTest.CanObtainSizeFromViewViaSize (0 ms)
29: [ RUN ] StringViewTest.CanObtainSizeFromViewViaLength
29: [ OK ] StringViewTest.CanObtainSizeFromViewViaLength (0 ms)
29: [ RUN ] StringViewTest.CanObtainMaxSizeViaMaxSize
29: [ OK ] StringViewTest.CanObtainMaxSizeViaMaxSize (0 ms)
29: [ RUN ] StringViewTest.CanCheckForEmptyStringWithEmpty
29: [ OK ] StringViewTest.CanCheckForEmptyStringWithEmpty (0 ms)
29: [ RUN ] StringViewTest.CanAccessElementViaArrayIndex
29: [ OK ] StringViewTest.CanAccessElementViaArrayIndex (0 ms)
29: [ RUN ] StringViewTest.CanAccessElementViaAt
29: [ OK ] StringViewTest.CanAccessElementViaAt (0 ms)
29: [ RUN ] StringViewTest.ThrowsOnOutOfBoundsAccess
29: [ OK ] StringViewTest.ThrowsOnOutOfBoundsAccess (0 ms)
29: [ RUN ] StringViewTest.CanAccessAllElementsViaData
29: [ OK ] StringViewTest.CanAccessAllElementsViaData (0 ms)
29: [ RUN ] StringViewTest.DataFromEmptyStringIsNullptr
29: [ OK ] StringViewTest.DataFromEmptyStringIsNullptr (0 ms)
29: [ RUN ] StringViewTest.CanRemovePrefix
29: [ OK ] StringViewTest.CanRemovePrefix (0 ms)
29: [ RUN ] StringViewTest.CanRemoveSuffix
29: [ OK ] StringViewTest.CanRemoveSuffix (0 ms)
29: [ RUN ] StringViewTest.CanSwapWithOtherView
29: [ OK ] StringViewTest.CanSwapWithOtherView (0 ms)
29: [ RUN ] StringViewTest.CanCopySubstringWithCopy
29: [ OK ] StringViewTest.CanCopySubstringWithCopy (0 ms)
29: [ RUN ] StringViewTest.ThrowsOnOutOfBoundsCopy
29: [ OK ] StringViewTest.ThrowsOnOutOfBoundsCopy (0 ms)
29: [ RUN ] StringViewTest.CanObtainSubstringWithSubstr
29: [ OK ] StringViewTest.CanObtainSubstringWithSubstr (0 ms)
29: [ RUN ] StringViewTest.ThrowsOnOutOfBoundsSubstr
29: [ OK ] StringViewTest.ThrowsOnOutOfBoundsSubstr (0 ms)
29: [ RUN ] StringViewTest.CanLexicallyCompareViewWithCompare
29: [ OK ] StringViewTest.CanLexicallyCompareViewWithCompare (0 ms)
29: [ RUN ] StringViewTest.CanCompareEmptyViewsWIthCompare
29: [ OK ] StringViewTest.CanCompareEmptyViewsWIthCompare (0 ms)
29: [ RUN ] StringViewTest.CanCompareSubStringWithViewViaCompare
29: [ OK ] StringViewTest.CanCompareSubStringWithViewViaCompare (0 ms)
29: [ RUN ] StringViewTest.CanCompareSubStringWithSubStringViewViaCompare
29: [ OK ] StringViewTest.CanCompareSubStringWithSubStringViewViaCompare (1 ms)
29: [ RUN ] StringViewTest.CanCompareToCStringViaCompare
29: [ OK ] StringViewTest.CanCompareToCStringViaCompare (0 ms)
29: [ RUN ] StringViewTest.CanCompareSubStringToCStringViaCompare
29: [ OK ] StringViewTest.CanCompareSubStringToCStringViaCompare (0 ms)
29: [ RUN ] StringViewTest.CanCompareSubStringToCStringPrefixViaCompare
29: [ OK ] StringViewTest.CanCompareSubStringToCStringPrefixViaCompare (0 ms)
29: [ RUN ] StringViewTest.CanCheckForPrefixViewViaStartsWith
29: [ OK ] StringViewTest.CanCheckForPrefixViewViaStartsWith (0 ms)
29: [ RUN ] StringViewTest.CanCheckForPrefixCharacterViaStartsWith
29: [ OK ] StringViewTest.CanCheckForPrefixCharacterViaStartsWith (0 ms)
29: [ RUN ] StringViewTest.CanCheckForPrefixCStringViaStartsWith
29: [ OK ] StringViewTest.CanCheckForPrefixCStringViaStartsWith (0 ms)
29: [ RUN ] StringViewTest.CanCheckForSuffixViewViaEndsWith
29: [ OK ] StringViewTest.CanCheckForSuffixViewViaEndsWith (0 ms)
29: [ RUN ] StringViewTest.CanCheckForSuffixCharacterViaEndsWith
29: [ OK ] StringViewTest.CanCheckForSuffixCharacterViaEndsWith (0 ms)
29: [ RUN ] StringViewTest.CanCheckForSuffixCStringViaEndsWith
29: [ OK ] StringViewTest.CanCheckForSuffixCStringViaEndsWith (0 ms)
29: [ RUN ] StringViewTest.CanSearchForViewSubstrViaFind
29: [ OK ] StringViewTest.CanSearchForViewSubstrViaFind (0 ms)
29: [ RUN ] StringViewTest.CanSearchForCharacterViaFind
29: [ OK ] StringViewTest.CanSearchForCharacterViaFind (0 ms)
29: [ RUN ] StringViewTest.CanSearchForCStringSubstringViaFind
29: [ OK ] StringViewTest.CanSearchForCStringSubstringViaFind (0 ms)
29: [ RUN ] StringViewTest.CanSearchForCStringSubstringViaFindWithDefaultPos
29: [ OK ] StringViewTest.CanSearchForCStringSubstringViaFindWithDefaultPos (0 ms)
29: [ RUN ] StringViewTest.CanBackwardsSearchForViewSubstrViaFind
29: [ OK ] StringViewTest.CanBackwardsSearchForViewSubstrViaFind (0 ms)
29: [ RUN ] StringViewTest.CanBackwardsSearchForCharacterViaFind
29: [ OK ] StringViewTest.CanBackwardsSearchForCharacterViaFind (0 ms)
29: [ RUN ] StringViewTest.CanBackwardsSearchForCStringSubstringViaFind
29: [ OK ] StringViewTest.CanBackwardsSearchForCStringSubstringViaFind (0 ms)
29: [ RUN ] StringViewTest.CanBackwardsSearchForCStringSubstringViaFindWithDefaultPos
29: [ OK ] StringViewTest.CanBackwardsSearchForCStringSubstringViaFindWithDefaultPos (0 ms)
29: [ RUN ] StringViewTest.CanSearchForFirstOccurenceOfAnyCharacterInView
29: [ OK ] StringViewTest.CanSearchForFirstOccurenceOfAnyCharacterInView (0 ms)
29: [ RUN ] StringViewTest.CanSearchForFirstOccurenceOfCharacter
29: [ OK ] StringViewTest.CanSearchForFirstOccurenceOfCharacter (0 ms)
29: [ RUN ] StringViewTest.CanSearchForFirstOccurenceOfCharactersInCStringInLenght
29: [ OK ] StringViewTest.CanSearchForFirstOccurenceOfCharactersInCStringInLenght (0 ms)
29: [ RUN ] StringViewTest.CanSearchForFirstOccurenceOfCharactersInCString
29: [ OK ] StringViewTest.CanSearchForFirstOccurenceOfCharactersInCString (0 ms)
29: [ RUN ] StringViewTest.CanBackwardsSearchForLastOccurenceOfAnyCharacterInView
29: [ OK ] StringViewTest.CanBackwardsSearchForLastOccurenceOfAnyCharacterInView (0 ms)
29: [ RUN ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharacter
29: [ OK ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharacter (0 ms)
29: [ RUN ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharactersInCStringInLenght
29: [ OK ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharactersInCStringInLenght (0 ms)
29: [ RUN ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharactersInCString
29: [ OK ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharactersInCString (0 ms)
29: [ RUN ] StringViewTest.CanSearchForFirstNotFoundCharacter
29: [ OK ] StringViewTest.CanSearchForFirstNotFoundCharacter (0 ms)
29: [ RUN ] StringViewTest.CanSearchForFirstNonMatchingCharacter
29: [ OK ] StringViewTest.CanSearchForFirstNonMatchingCharacter (0 ms)
29: [ RUN ] StringViewTest.CanSearchForFirstNonEqualToAnyCharacterInCStringInLength
29: [ OK ] StringViewTest.CanSearchForFirstNonEqualToAnyCharacterInCStringInLength (1 ms)
29: [ RUN ] StringViewTest.CanSearchForFirstNonEqualToAnyCharacterInCString
29: [ OK ] StringViewTest.CanSearchForFirstNonEqualToAnyCharacterInCString (0 ms)
29: [ RUN ] StringViewTest.CanBackwardsSearchForForstNonFoundCharacterInView
29: [ OK ] StringViewTest.CanBackwardsSearchForForstNonFoundCharacterInView (0 ms)
29: [ RUN ] StringViewTest.CanBackwardsSearchForFirstNonMatchingCharacter
29: [ OK ] StringViewTest.CanBackwardsSearchForFirstNonMatchingCharacter (0 ms)
29: [ RUN ] StringViewTest.CanBackwardsSearchForFirstNonEqualToAnyCharacterInCStringInLength
29: [ OK ] StringViewTest.CanBackwardsSearchForFirstNonEqualToAnyCharacterInCStringInLength (0 ms)
29: [ RUN ] StringViewTest.CanBackwardsSearchForFirstNonEqualToAnyCharacterInCString
29: [ OK ] StringViewTest.CanBackwardsSearchForFirstNonEqualToAnyCharacterInCString (0 ms)
29: [ RUN ] StringViewTest.CanCreateViewWithLiteralSV
29: [ OK ] StringViewTest.CanCreateViewWithLiteralSV (0 ms)
29: [ RUN ] StringViewTest.CanCreateViewWithLiteralSVInLiteralsStringViewLiteralsNamespace
29: [ OK ] StringViewTest.CanCreateViewWithLiteralSVInLiteralsStringViewLiteralsNamespace (0 ms)
29: [ RUN ] StringViewTest.CanCreateViewWithLiteralSVInStringViewLiteralsNamespace
29: [ OK ] StringViewTest.CanCreateViewWithLiteralSVInStringViewLiteralsNamespace (0 ms)
29: [ RUN ] StringViewTest.CanCreateViewWithLiteralSVInLiteralsNamespace
29: [ OK ] StringViewTest.CanCreateViewWithLiteralSVInLiteralsNamespace (0 ms)
29: [ RUN ] StringViewTest.CanCreateViewWithLiteral_SV
29: [ OK ] StringViewTest.CanCreateViewWithLiteral_SV (0 ms)
29: [ RUN ] StringViewTest.CanCreateViewWithLiteral_SVInLiteralsStringViewLiteralsNamespace
29: [ OK ] StringViewTest.CanCreateViewWithLiteral_SVInLiteralsStringViewLiteralsNamespace (0 ms)
29: [ RUN ] StringViewTest.CanCreateViewWithLiteral_SVInStringViewLiteralsNamespace
29: [ OK ] StringViewTest.CanCreateViewWithLiteral_SVInStringViewLiteralsNamespace (0 ms)
29: [ RUN ] StringViewTest.CanCreateViewWithLiteral_SVInLiteralsNamespace
29: [ OK ] StringViewTest.CanCreateViewWithLiteral_SVInLiteralsNamespace (0 ms)
29: [ RUN ] StringViewTest.CanCompareToViews
29: [ OK ] StringViewTest.CanCompareToViews (0 ms)
29: [ RUN ] StringViewTest.CanCompareViewToImplicitlyConvertedView
29: [ OK ] StringViewTest.CanCompareViewToImplicitlyConvertedView (0 ms)
29: [ RUN ] StringViewTest.EmptyViewsCompareAsEqual
29: [ OK ] StringViewTest.EmptyViewsCompareAsEqual (0 ms)
29: [ RUN ] StringViewTest.CanPrintViewToPutputStream
29: [ OK ] StringViewTest.CanPrintViewToPutputStream (0 ms)
29: [ RUN ] StringViewTest.HashOfViewIsEqualToHashOfString
29: [ OK ] StringViewTest.HashOfViewIsEqualToHashOfString (0 ms)
29: [ RUN ] StringViewTest.HashOfWStringViewIsEqualToHashOfString
29: [ OK ] StringViewTest.HashOfWStringViewIsEqualToHashOfString (0 ms)
29: [ RUN ] StringViewTest.HashOfU16StringViewIsEqualToHashOfString
29: [ OK ] StringViewTest.HashOfU16StringViewIsEqualToHashOfString (0 ms)
29: [ RUN ] StringViewTest.HashOfU32StringViewIsEqualToHashOfString
29: [ OK ] StringViewTest.HashOfU32StringViewIsEqualToHashOfString (0 ms)
29: [----------] 80 tests from StringViewTest (6 ms total)
29:
29: [----------] 5 tests from StringViewExtensionTest
29: [ RUN ] StringViewExtensionTest.CanConstructViewFromString
29: [ OK ] StringViewExtensionTest.CanConstructViewFromString (0 ms)
29: [ RUN ] StringViewExtensionTest.CanConvertViewToStringViaExplicitOperator
29: [ OK ] StringViewExtensionTest.CanConvertViewToStringViaExplicitOperator (0 ms)
29: [ RUN ] StringViewExtensionTest.CanConvertViewToStringViaToString
29: [ OK ] StringViewExtensionTest.CanConvertViewToStringViaToString (0 ms)
29: [ RUN ] StringViewExtensionTest.CanConvertViewToStringViaToStringFreeFunction
29: [ OK ] StringViewExtensionTest.CanConvertViewToStringViaToStringFreeFunction (0 ms)
29: [ RUN ] StringViewExtensionTest.CanConvertViewToStringViewViaToStringView
29: [ OK ] StringViewExtensionTest.CanConvertViewToStringViewViaToStringView (0 ms)
29: [----------] 5 tests from StringViewExtensionTest (0 ms total)
29:
29: [----------] Global test environment tear-down
29: [==========] 170 tests from 12 test cases ran. (15 ms total)
29: [ PASSED ] 170 tests.
29/52 Test #29: CompatibilityHelpersTests ........... Passed 0.09 sec
test 30
Start 30: GmxAnaTest
30: Test command: /<<PKGBUILDDIR>>/build/basic/bin/gmxana-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/GmxAnaTest.xml"
30: Test timeout computed to be: 600
30: [==========] Running 27 tests from 5 test cases.
30: [----------] Global test environment set-up.
30: [----------] 5 tests from Entropy
30: [ RUN ] Entropy.Schlitter_300_NoLinear
30: [ OK ] Entropy.Schlitter_300_NoLinear (19 ms)
30: [ RUN ] Entropy.Schlitter_300_Linear
30: [ OK ] Entropy.Schlitter_300_Linear (0 ms)
30: [ RUN ] Entropy.QuasiHarmonic_300_NoLinear
30: [ OK ] Entropy.QuasiHarmonic_300_NoLinear (1 ms)
30: [ RUN ] Entropy.QuasiHarmonic_200_NoLinear
30: [ OK ] Entropy.QuasiHarmonic_200_NoLinear (1 ms)
30: [ RUN ] Entropy.QuasiHarmonic_200_Linear
30: [ OK ] Entropy.QuasiHarmonic_200_Linear (1 ms)
30: [----------] 5 tests from Entropy (23 ms total)
30:
30: [----------] 10 tests from MindistTest
30: [ RUN ] MindistTest.mindistWorksWithSingleAtoms
30: Group 0 ( atom1) has 1 elements
30: Group 1 ( atom2) has 1 elements
30: Group 2 ( atom3) has 1 elements
30: Group 3 ( atoms12) has 2 elements
30: Group 4 ( atoms23) has 2 elements
30: Group 5 ( atoms123) has 3 elements
30: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
30:
Reading frame 0 time 0.000
Last frame 0 time 0.000
30: Selected 0: 'atom1'
30: Selected 1: 'atom2'
30: [ OK ] MindistTest.mindistWorksWithSingleAtoms (20 ms)
30: [ RUN ] MindistTest.mindistWorksWithMultipleAtoms
30: Group 0 ( atom1) has 1 elements
30: Group 1 ( atom2) has 1 elements
30: Group 2 ( atom3) has 1 elements
30: Group 3 ( atoms12) has 2 elements
30: Group 4 ( atoms23) has 2 elements
30: Group 5 ( atoms123) has 3 elements
30: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
30:
Reading frame 0 time 0.000
Last frame 0 time 0.000
30: Selected 2: 'atom3'
30: Selected 3: 'atoms12'
30: [ OK ] MindistTest.mindistWorksWithMultipleAtoms (5 ms)
30: [ RUN ] MindistTest.mindistDoesNotPickUpContacts
30: Group 0 ( atom1) has 1 elements
30: Group 1 ( atom2) has 1 elements
30: Group 2 ( atom3) has 1 elements
30: Group 3 ( atoms12) has 2 elements
30: Group 4 ( atoms23) has 2 elements
30: Group 5 ( atoms123) has 3 elements
30: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
30:
Reading frame 0 time 0.000
Last frame 0 time 0.000
30: Selected 0: 'atom1'
30: Selected 1: 'atom2'
30: [ OK ] MindistTest.mindistDoesNotPickUpContacts (6 ms)
30: [ RUN ] MindistTest.mindistPicksUpContacts
30: Group 0 ( atom1) has 1 elements
30: Group 1 ( atom2) has 1 elements
30: Group 2 ( atom3) has 1 elements
30: Group 3 ( atoms12) has 2 elements
30: Group 4 ( atoms23) has 2 elements
30: Group 5 ( atoms123) has 3 elements
30: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
30:
Reading frame 0 time 0.000
Last frame 0 time 0.000
30: Selected 0: 'atom1'
30: Selected 1: 'atom2'
30: [ OK ] MindistTest.mindistPicksUpContacts (5 ms)
30: [ RUN ] MindistTest.ngWorks
30: Group 0 ( atom1) has 1 elements
30: Group 1 ( atom2) has 1 elements
30: Group 2 ( atom3) has 1 elements
30: Group 3 ( atoms12) has 2 elements
30: Group 4 ( atoms23) has 2 elements
30: Group 5 ( atoms123) has 3 elements
30: Select a group: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
30:
Reading frame 0 time 0.000
Last frame 0 time 0.000
30: Selected 0: 'atom1'
30: Selected 1: 'atom2'
30: Selected 2: 'atom3'
30: [ OK ] MindistTest.ngWorks (5 ms)
30: [ RUN ] MindistTest.groupWorks
30: Group 0 ( atom1) has 1 elements
30: Group 1 ( atom2) has 1 elements
30: Group 2 ( atom3) has 1 elements
30: Group 3 ( atoms12) has 2 elements
30: Group 4 ( atoms23) has 2 elements
30: Group 5 ( atoms123) has 3 elements
30: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
30:
Reading frame 0 time 0.000
Last frame 0 time 0.000
30: Selected 3: 'atoms12'
30: Selected 2: 'atom3'
30: [ OK ] MindistTest.groupWorks (6 ms)
30: [ RUN ] MindistTest.maxDistWorks
30: Group 0 ( atom1) has 1 elements
30: Group 1 ( atom2) has 1 elements
30: Group 2 ( atom3) has 1 elements
30: Group 3 ( atoms12) has 2 elements
30: Group 4 ( atoms23) has 2 elements
30: Group 5 ( atoms123) has 3 elements
30: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
30:
Reading frame 0 time 0.000
Last frame 0 time 0.000
30: Selected 2: 'atom3'
30: Selected 3: 'atoms12'
30: [ OK ] MindistTest.maxDistWorks (4 ms)
30: [ RUN ] MindistTest.noPbcWorks
30: Group 0 ( atom1) has 1 elements
30: Group 1 ( atom2) has 1 elements
30: Group 2 ( atom3) has 1 elements
30: Group 3 ( atoms12) has 2 elements
30: Group 4 ( atoms23) has 2 elements
30: Group 5 ( atoms123) has 3 elements
30: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
30:
Reading frame 0 time 0.000
Last frame 0 time 0.000
30: Selected 0: 'atom1'
30: Selected 1: 'atom2'
30: [ OK ] MindistTest.noPbcWorks (4 ms)
30: [ RUN ] MindistTest.resPerTimeWorks
30: Group 0 ( atom1) has 1 elements
30: Group 1 ( atom2) has 1 elements
30: Group 2 ( atom3) has 1 elements
30: Group 3 ( atoms12) has 2 elements
30: Group 4 ( atoms23) has 2 elements
30: Group 5 ( atoms123) has 3 elements
30: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
30:
Reading frame 0 time 0.000
Last frame 0 time 0.000
30: Selected 3: 'atoms12'
30: Selected 2: 'atom3'
30: [ OK ] MindistTest.resPerTimeWorks (6 ms)
30: [ RUN ] MindistTest.matrixWorks
30: Group 0 ( atom1) has 1 elements
30: Group 1 ( atom2) has 1 elements
30: Group 2 ( atom3) has 1 elements
30: Group 3 ( atoms12) has 2 elements
30: Group 4 ( atoms23) has 2 elements
30: Group 5 ( atoms123) has 3 elements
30: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
30:
Reading frame 0 time 0.000
Last frame 0 time 0.000
30: Selected 5: 'atoms123'
30: Special case: making distance matrix between all atoms in group atoms123
30: [ OK ] MindistTest.matrixWorks (5 ms)
30: [----------] 10 tests from MindistTest (67 ms total)
30:
30: [----------] 3 tests from MsdTest
30: [ RUN ] MsdTest.threeDimensionalDiffusion
30:
30: Select a group to calculate mean squared displacement for:
30: Group 0 ( particles) has 3 elements
30: There is one group in the index
30:
Reading frame 0 time 0.000
Reading frame 1 time 1.000
Reading frame 2 time 2.000
Reading frame 3 time 3.000
Reading frame 4 time 4.000
Reading frame 5 time 5.000
Reading frame 6 time 6.000
Reading frame 7 time 7.000
Reading frame 8 time 8.000
Reading frame 9 time 9.000
Last frame 9 time 9.000
30:
30: Used 1 restart points spaced 200 ps over 9 ps
30:
30: Fitting from 1 to 8 ps
30:
30: D[ particles] 4.0000 (+/- 0.0000) 1e-5 cm^2/s
30: [ OK ] MsdTest.threeDimensionalDiffusion (6 ms)
30: [ RUN ] MsdTest.twoDimensionalDiffusion
30:
30: Select a group to calculate mean squared displacement for:
30: Group 0 ( particles) has 3 elements
30: There is one group in the index
30:
Reading frame 0 time 0.000
Reading frame 1 time 1.000
Reading frame 2 time 2.000
Reading frame 3 time 3.000
Reading frame 4 time 4.000
Reading frame 5 time 5.000
Reading frame 6 time 6.000
Reading frame 7 time 7.000
Reading frame 8 time 8.000
Reading frame 9 time 9.000
Last frame 9 time 9.000
30:
30: Used 1 restart points spaced 200 ps over 9 ps
30:
30: Fitting from 1 to 8 ps
30:
30: D[ particles] 6.0000 (+/- 0.0000) 1e-5 cm^2/s
30: [ OK ] MsdTest.twoDimensionalDiffusion (4 ms)
30: [ RUN ] MsdTest.oneDimensionalDiffusion
30:
30: Select a group to calculate mean squared displacement for:
30: Group 0 ( particles) has 3 elements
30: There is one group in the index
30:
Reading frame 0 time 0.000
Reading frame 1 time 1.000
Reading frame 2 time 2.000
Reading frame 3 time 3.000
Reading frame 4 time 4.000
Reading frame 5 time 5.000
Reading frame 6 time 6.000
Reading frame 7 time 7.000
Reading frame 8 time 8.000
Reading frame 9 time 9.000
Last frame 9 time 9.000
30:
30: Used 1 restart points spaced 200 ps over 9 ps
30:
30: Fitting from 1 to 8 ps
30:
30: D[ particles] 8.0000 (+/- 0.0000) 1e-5 cm^2/s
30: [ OK ] MsdTest.oneDimensionalDiffusion (4 ms)
30: [----------] 3 tests from MsdTest (17 ms total)
30:
30: [----------] 3 tests from MsdMolTest
30: [ RUN ] MsdMolTest.diffMolMassWeighted
30:
30: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.mdp]:
30: For a correct single-point energy evaluation with nsteps = 0, use
30: continuation = yes to avoid constraining the input coordinates.
30:
30: Setting the LD random seed to 1513365098
30: Generated 330891 of the 330891 non-bonded parameter combinations
30: Generating 1-4 interactions: fudge = 0.5
30: Generated 330891 of the 330891 1-4 parameter combinations
30: Excluding 2 bonded neighbours molecule type 'SOL'
30: Number of degrees of freedom in T-Coupling group rest is 27.00
30:
30: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.mdp]:
30: NVE simulation with an initial temperature of zero: will use a Verlet
30: buffer of 10%. Check your energy drift!
30:
30:
30: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.mdp]:
30: You are using a plain Coulomb cut-off, which might produce artifacts.
30: You might want to consider using PME electrostatics.
30:
30:
30:
30: There were 3 notes
30: Calculating diffusion coefficients for molecules.
30: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
30: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
30:
30: Select a group to calculate mean squared displacement for:
30: Group 0 ( water) has 15 elements
30: There is one group in the index
30: Split group of 15 atoms into 5 molecules
30: Reading frames from pdb file
Reading frame 0 time 0.000 'water t= 0.00400 step= 20', 15 atoms
30:
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Reading frame 5 time 0.020
Reading frame 6 time 0.024
Reading frame 7 time 0.028
Reading frame 8 time 0.032
Reading frame 9 time 0.036
Reading frame 10 time 0.040
Reading frame 11 time 0.044
Reading frame 12 time 0.048
Reading frame 13 time 0.052
Reading frame 14 time 0.056
Reading frame 15 time 0.060
Reading frame 16 time 0.064
Reading frame 17 time 0.068
Reading frame 18 time 0.072
Reading frame 19 time 0.076
Reading frame 20 time 0.080
30:
30: Used 1 restart points spaced 200 ps over 0.1 ps
30:
30: This run will generate roughly 0 Mb of data
30: <D> = 6.4731 Std. Dev. = 8.0969 Error = 3.6210
30: Fitting from 0.008 to 0.088 ps
30:
30: D[ water] 6.5741 (+/- 0.7753) 1e-5 cm^2/s
30: [ OK ] MsdMolTest.diffMolMassWeighted (3195 ms)
30: [ RUN ] MsdMolTest.diffMolNonMassWeighted
30:
30: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.mdp]:
30: For a correct single-point energy evaluation with nsteps = 0, use
30: continuation = yes to avoid constraining the input coordinates.
30:
30: Setting the LD random seed to 948533642
30: Generated 330891 of the 330891 non-bonded parameter combinations
30: Generating 1-4 interactions: fudge = 0.5
30: Generated 330891 of the 330891 1-4 parameter combinations
30: Excluding 2 bonded neighbours molecule type 'SOL'
30: Number of degrees of freedom in T-Coupling group rest is 27.00
30:
30: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.mdp]:
30: NVE simulation with an initial temperature of zero: will use a Verlet
30: buffer of 10%. Check your energy drift!
30:
30:
30: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.mdp]:
30: You are using a plain Coulomb cut-off, which might produce artifacts.
30: You might want to consider using PME electrostatics.
30:
30:
30:
30: There were 3 notes
30: Calculating diffusion coefficients for molecules.
30: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
30: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
30:
30: Select a group to calculate mean squared displacement for:
30: Group 0 ( water) has 15 elements
30: There is one group in the index
30: Split group of 15 atoms into 5 molecules
30: Reading frames from pdb file
Reading frame 0 time 0.000 'water t= 0.00400 step= 20', 15 atoms
30:
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Reading frame 5 time 0.020
Reading frame 6 time 0.024
Reading frame 7 time 0.028
Reading frame 8 time 0.032
Reading frame 9 time 0.036
Reading frame 10 time 0.040
Reading frame 11 time 0.044
Reading frame 12 time 0.048
Reading frame 13 time 0.052
Reading frame 14 time 0.056
Reading frame 15 time 0.060
Reading frame 16 time 0.064
Reading frame 17 time 0.068
Reading frame 18 time 0.072
Reading frame 19 time 0.076
Reading frame 20 time 0.080
30:
30: Used 1 restart points spaced 200 ps over 0.1 ps
30:
30: This run will generate roughly 0 Mb of data
30: <D> = 6.4731 Std. Dev. = 8.0969 Error = 3.6210
30: Fitting from 0.008 to 0.088 ps
30:
30: D[ water] 6.5741 (+/- 0.7753) 1e-5 cm^2/s
30: [ OK ] MsdMolTest.diffMolNonMassWeighted (3140 ms)
30: [ RUN ] MsdMolTest.diffMolSelected
30:
30: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.mdp]:
30: For a correct single-point energy evaluation with nsteps = 0, use
30: continuation = yes to avoid constraining the input coordinates.
30:
30: Setting the LD random seed to -212101098
30: Generated 330891 of the 330891 non-bonded parameter combinations
30: Generating 1-4 interactions: fudge = 0.5
30: Generated 330891 of the 330891 1-4 parameter combinations
30: Excluding 2 bonded neighbours molecule type 'SOL'
30: Number of degrees of freedom in T-Coupling group rest is 27.00
30:
30: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.mdp]:
30: NVE simulation with an initial temperature of zero: will use a Verlet
30: buffer of 10%. Check your energy drift!
30:
30:
30: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.mdp]:
30: You are using a plain Coulomb cut-off, which might produce artifacts.
30: You might want to consider using PME electrostatics.
30:
30:
30:
30: There were 3 notes
30: Calculating diffusion coefficients for molecules.
30: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
30: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
30:
30: Select a group to calculate mean squared displacement for:
30: Group 0 ( mol) has 9 elements
30: There is one group in the index
30: Split group of 9 atoms into 3 molecules
30: Reading frames from pdb file
Reading frame 0 time 0.000 'water t= 0.00400 step= 20', 15 atoms
30:
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Reading frame 5 time 0.020
Reading frame 6 time 0.024
Reading frame 7 time 0.028
Reading frame 8 time 0.032
Reading frame 9 time 0.036
Reading frame 10 time 0.040
Reading frame 11 time 0.044
Reading frame 12 time 0.048
Reading frame 13 time 0.052
Reading frame 14 time 0.056
Reading frame 15 time 0.060
Reading frame 16 time 0.064
Reading frame 17 time 0.068
Reading frame 18 time 0.072
Reading frame 19 time 0.076
Reading frame 20 time 0.080
30:
30: Used 1 restart points spaced 200 ps over 0.1 ps
30:
30: This run will generate roughly 0 Mb of data
30: <D> = 7.3593 Std. Dev. = 9.7910 Error = 5.6529
30: Fitting from 0.008 to 0.088 ps
30:
30: D[ mol] 7.8614 (+/- 1.5618) 1e-5 cm^2/s
30: [ OK ] MsdMolTest.diffMolSelected (3121 ms)
30: [----------] 3 tests from MsdMolTest (9457 ms total)
30:
30: [----------] 6 tests from NoFatalErrorWhenWritingFrom/GmxTraj
30: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0
30: Group 0 ( System) has 6 elements
30: Group 1 ( Water) has 6 elements
30: Group 2 ( SOL) has 6 elements
30: Select a group: trr version: GMX_trn_file (single precision)
30:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
30: Selected 0: 'System'
30: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 (34 ms)
30: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1
30: Group 0 ( System) has 6 elements
30: Group 1 ( Water) has 6 elements
30: Group 2 ( SOL) has 6 elements
30: Select a group:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
30: Selected 0: 'System'
30: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 (11 ms)
30: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2
30: Group 0 ( System) has 6 elements
30: Group 1 ( Water) has 6 elements
30: Group 2 ( SOL) has 6 elements
30: Select a group:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
30: Selected 0: 'System'
30: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 (9 ms)
30: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3
30: Group 0 ( System) has 6 elements
30: Group 1 ( Water) has 6 elements
30: Group 2 ( SOL) has 6 elements
30: Select a group: Reading frames from gro file '', 6 atoms.
30:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
30: Selected 0: 'System'
30: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 (9 ms)
30: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4
30: Group 0 ( System) has 6 elements
30: Group 1 ( Water) has 6 elements
30: Group 2 ( SOL) has 6 elements
30: Select a group: Reading frames from pdb file
Reading frame 0 time 0.000 't= 0.00000', 6 atoms
30:
Reading frame 1 time 0.000
Last frame 1 time 0.000
30: Selected 0: 'System'
30: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 (9 ms)
30: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5
30: Group 0 ( System) has 6 elements
30: Group 1 ( Water) has 6 elements
30: Group 2 ( SOL) has 6 elements
30: Select a group:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
30: Selected 0: 'System'
30: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 (10 ms)
30: [----------] 6 tests from NoFatalErrorWhenWritingFrom/GmxTraj (85 ms total)
30:
30: [----------] Global test environment tear-down
30: [==========] 27 tests from 5 test cases ran. (9652 ms total)
30: [ PASSED ] 27 tests.
30/52 Test #30: GmxAnaTest .......................... Passed 9.73 sec
test 31
Start 31: GmxPreprocessTests
31: Test command: /<<PKGBUILDDIR>>/build/basic/bin/gmxpreprocess-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/GmxPreprocessTests.xml"
31: Test timeout computed to be: 30
31: [==========] Running 69 tests from 10 test cases.
31: [----------] Global test environment set-up.
31: [----------] 4 tests from GenconfTest
31: [ RUN ] GenconfTest.nbox_Works
31: [ OK ] GenconfTest.nbox_Works (17 ms)
31: [ RUN ] GenconfTest.nbox_norenumber_Works
31: [ OK ] GenconfTest.nbox_norenumber_Works (5 ms)
31: [ RUN ] GenconfTest.nbox_dist_Works
31: [ OK ] GenconfTest.nbox_dist_Works (15 ms)
31: [ RUN ] GenconfTest.nbox_rot_Works
31: center of geometry: 1.733667, 1.477000, 0.905167
31: center of geometry: 1.733667, 1.477000, 0.905167
31: center of geometry: 1.733667, 1.477000, 0.905167
31: center of geometry: 1.733667, 1.477000, 0.905167
31: center of geometry: 1.733667, 1.477000, 0.905167
31: center of geometry: 1.733667, 1.477000, 0.905167
31: center of geometry: 1.733667, 1.477000, 0.905167
31: center of geometry: 1.733667, 1.477000, 0.905167
31: center of geometry: 1.733667, 1.477000, 0.905167
31: center of geometry: 1.733667, 1.477000, 0.905167
31: center of geometry: 1.733667, 1.477000, 0.905167
31: center of geometry: 1.733667, 1.477000, 0.905167
31: [ OK ] GenconfTest.nbox_rot_Works (8 ms)
31: [----------] 4 tests from GenconfTest (45 ms total)
31:
31: [----------] 2 tests from GenionTest
31: [ RUN ] GenionTest.HighConcentrationIonPlacement
31:
31: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]:
31: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet
31: buffer. The cluster pair list does have a buffering effect, but choosing
31: a larger rlist might be necessary for good energy conservation.
31:
31:
31: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]:
31: For a correct single-point energy evaluation with nsteps = 0, use
31: continuation = yes to avoid constraining the input coordinates.
31:
31: Setting the LD random seed to -337564225
31: Generated 331705 of the 331705 non-bonded parameter combinations
31: Generating 1-4 interactions: fudge = 0.5
31: Generated 331705 of the 331705 1-4 parameter combinations
31: Excluding 2 bonded neighbours molecule type 'SOL'
31: Excluding 3 bonded neighbours molecule type 'methane'
31: Number of degrees of freedom in T-Coupling group rest is 1308.00
31:
31: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]:
31: You are using a plain Coulomb cut-off, which might produce artifacts.
31: You might want to consider using PME electrostatics.
31:
31:
31:
31: There were 3 notes
31: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
31: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
31: Group 0 ( System) has 653 elements
31: Group 1 ( Water) has 648 elements
31: Group 2 ( SOL) has 648 elements
31: Group 3 ( non-Water) has 5 elements
31: Group 4 ( Other) has 5 elements
31: Group 5 ( METH) has 5 elements
31: Select a group: Number of (3-atomic) solvent molecules: 216
31: Using random seed 1997.
31: Replacing solvent molecule 56 (atom 168) with NA
31: Replacing solvent molecule 120 (atom 360) with NA
31: Replacing solvent molecule 182 (atom 546) with NA
31: Replacing solvent molecule 71 (atom 213) with NA
31: Replacing solvent molecule 189 (atom 567) with CL
31: Replacing solvent molecule 54 (atom 162) with CL
31: Replacing solvent molecule 155 (atom 465) with CL
31: Replacing solvent molecule 99 (atom 297) with CL
31:
31: Analysing residue names:
31: There are: 216 Water residues
31: There are: 1 Other residues
31: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
31: This run will generate roughly 0 Mb of data
31: Will try to add 4 NA ions and 4 CL ions.
31: Select a continuous group of solvent molecules
31: Selected 1: 'Water'
31: [ OK ] GenionTest.HighConcentrationIonPlacement (3186 ms)
31: [ RUN ] GenionTest.NoIonPlacement
31:
31: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]:
31: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet
31: buffer. The cluster pair list does have a buffering effect, but choosing
31: a larger rlist might be necessary for good energy conservation.
31:
31:
31: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]:
31: For a correct single-point energy evaluation with nsteps = 0, use
31: continuation = yes to avoid constraining the input coordinates.
31:
31: Setting the LD random seed to 583615082
31: Generated 331705 of the 331705 non-bonded parameter combinations
31: Generating 1-4 interactions: fudge = 0.5
31: Generated 331705 of the 331705 1-4 parameter combinations
31: Excluding 2 bonded neighbours molecule type 'SOL'
31: Excluding 3 bonded neighbours molecule type 'methane'
31: Number of degrees of freedom in T-Coupling group rest is 1308.00
31:
31: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]:
31: You are using a plain Coulomb cut-off, which might produce artifacts.
31: You might want to consider using PME electrostatics.
31:
31:
31:
31: There were 3 notes
31: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
31: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
31: No ions to add, will just copy input configuration.
31: Analysing residue names:
31: There are: 216 Water residues
31: There are: 1 Other residues
31: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
31: This run will generate roughly 0 Mb of data
31: [ OK ] GenionTest.NoIonPlacement (3163 ms)
31: [----------] 2 tests from GenionTest (6349 ms total)
31:
31: [----------] 1 test from GenRestrTest
31: [ RUN ] GenRestrTest.SimpleRestraintsGenerated
31:
31: Reading structure file
31: Group 0 ( System) has 156 elements
31: Group 1 ( Protein) has 156 elements
31: Group 2 ( Protein-H) has 75 elements
31: Group 3 ( C-alpha) has 10 elements
31: Group 4 ( Backbone) has 30 elements
31: Group 5 ( MainChain) has 40 elements
31: Group 6 ( MainChain+Cb) has 49 elements
31: Group 7 ( MainChain+H) has 52 elements
31: Group 8 ( SideChain) has 104 elements
31: Group 9 ( SideChain-H) has 35 elements
31: Select a group: Select group to position restrain
31: Selected 3: 'C-alpha'
31: [ OK ] GenRestrTest.SimpleRestraintsGenerated (28 ms)
31: [----------] 1 test from GenRestrTest (28 ms total)
31:
31: [----------] 9 tests from PreprocessingAtomTypesTest
31: [ RUN ] PreprocessingAtomTypesTest.EmptyOnCreate
31: [ OK ] PreprocessingAtomTypesTest.EmptyOnCreate (0 ms)
31: [ RUN ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid
31: [ OK ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid (0 ms)
31: [ RUN ] PreprocessingAtomTypesTest.AddTypeWorks
31: [ OK ] PreprocessingAtomTypesTest.AddTypeWorks (0 ms)
31: [ RUN ] PreprocessingAtomTypesTest.AddMultipleTypesWorks
31: [ OK ] PreprocessingAtomTypesTest.AddMultipleTypesWorks (0 ms)
31: [ RUN ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry
31: [ OK ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry (1 ms)
31: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFound
31: [ OK ] PreprocessingAtomTypesTest.CorrectNameFound (0 ms)
31: [ RUN ] PreprocessingAtomTypesTest.WrongNameNotFound
31: [ OK ] PreprocessingAtomTypesTest.WrongNameNotFound (0 ms)
31: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber
31: [ OK ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber (0 ms)
31: [ RUN ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber
31: [ OK ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber (0 ms)
31: [----------] 9 tests from PreprocessingAtomTypesTest (1 ms total)
31:
31: [----------] 10 tests from PreprocessingBondAtomTypeTest
31: [ RUN ] PreprocessingBondAtomTypeTest.EmptyOnCreate
31: [ OK ] PreprocessingBondAtomTypeTest.EmptyOnCreate (0 ms)
31: [ RUN ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid
31: [ OK ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid (0 ms)
31: [ RUN ] PreprocessingBondAtomTypeTest.AddTypeWorks
31: [ OK ] PreprocessingBondAtomTypeTest.AddTypeWorks (0 ms)
31: [ RUN ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks
31: [ OK ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks (0 ms)
31: [ RUN ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry
31: [ OK ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry (0 ms)
31: [ RUN ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType
31: [ OK ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType (0 ms)
31: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFound
31: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFound (0 ms)
31: [ RUN ] PreprocessingBondAtomTypeTest.WrongNameNotFound
31: [ OK ] PreprocessingBondAtomTypeTest.WrongNameNotFound (0 ms)
31: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber
31: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber (0 ms)
31: [ RUN ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber
31: [ OK ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber (0 ms)
31: [----------] 10 tests from PreprocessingBondAtomTypeTest (0 ms total)
31:
31: [----------] 5 tests from InsertMoleculesTest
31: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration
31: Reading solute configuration
31: Initialising inter-atomic distances...
31:
31: WARNING: Masses and atomic (Van der Waals) radii will be guessed
31: based on residue and atom names, since they could not be
31: definitively assigned from the information in your input
31: files. These guessed numbers might deviate from the mass
31: and radius of the atom type. Please check the output
31: files if necessary.
31:
31: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
31: from the source below. This means the results may be different
31: compared to previous GROMACS versions.
31:
31: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
31: A. Bondi
31: van der Waals Volumes and Radii
31: J. Phys. Chem. 68 (1964) pp. 441-451
31: -------- -------- --- Thank You --- -------- --------
31:
31: Using random seed 1997
31:
Try 1 success (now 8 atoms)!
31:
31: Added 1 molecules (out of 1 requested)
31: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoExistingConfiguration_out.gro
31:
31: Output configuration contains 8 atoms in 4 residues
31: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration (39 ms)
31: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox
31: Initialising inter-atomic distances...
31:
31: WARNING: Masses and atomic (Van der Waals) radii will be guessed
31: based on residue and atom names, since they could not be
31: definitively assigned from the information in your input
31: files. These guessed numbers might deviate from the mass
31: and radius of the atom type. Please check the output
31: files if necessary.
31:
31: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
31: from the source below. This means the results may be different
31: compared to previous GROMACS versions.
31:
31: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
31: A. Bondi
31: van der Waals Volumes and Radii
31: J. Phys. Chem. 68 (1964) pp. 441-451
31: -------- -------- --- Thank You --- -------- --------
31:
31: Using random seed 1997
31:
Try 1 success (now 2 atoms)!
31:
Try 2 success (now 4 atoms)!
31:
Try 3 success (now 6 atoms)!
31:
Try 4 success (now 8 atoms)!
31:
Try 5 success (now 10 atoms)!
31:
31: Added 5 molecules (out of 5 requested)
31: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEmptyBox_out.gro
31:
31: Output configuration contains 10 atoms in 10 residues
31: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox (8 ms)
31: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox
31: Reading solute configuration
31: Initialising inter-atomic distances...
31:
31: WARNING: Masses and atomic (Van der Waals) radii will be guessed
31: based on residue and atom names, since they could not be
31: definitively assigned from the information in your input
31: files. These guessed numbers might deviate from the mass
31: and radius of the atom type. Please check the output
31: files if necessary.
31:
31: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
31: from the source below. This means the results may be different
31: compared to previous GROMACS versions.
31:
31: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
31: A. Bondi
31: van der Waals Volumes and Radii
31: J. Phys. Chem. 68 (1964) pp. 441-451
31: -------- -------- --- Thank You --- -------- --------
31:
31: Using random seed 1997
31:
Try 1 success (now 8 atoms)!
31:
Try 2 success (now 10 atoms)!
31:
31: Added 2 molecules (out of 2 requested)
31: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEnlargedBox_out.gro
31:
31: Output configuration contains 10 atoms in 4 residues
31: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox (9 ms)
31: [ RUN ] InsertMoleculesTest.InsertsMoleculesWithReplacement
31: Reading solute configuration
31: Initialising inter-atomic distances...
31:
31: WARNING: Masses and atomic (Van der Waals) radii will be guessed
31: based on residue and atom names, since they could not be
31: definitively assigned from the information in your input
31: files. These guessed numbers might deviate from the mass
31: and radius of the atom type. Please check the output
31: files if necessary.
31:
31: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
31: from the source below. This means the results may be different
31: compared to previous GROMACS versions.
31:
31: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
31: A. Bondi
31: van der Waals Volumes and Radii
31: J. Phys. Chem. 68 (1964) pp. 441-451
31: -------- -------- --- Thank You --- -------- --------
31:
31: Using random seed 1997
31:
Try 1 success (now 650 atoms)!
31:
Try 2 success (now 652 atoms)!
31:
Try 3 success (now 654 atoms)!
31:
Try 4 success (now 656 atoms)!
31:
31: Added 4 molecules (out of 4 requested)
31: Replaced 8 residues (24 atoms)
31: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesWithReplacement_out.gro
31:
31: Output configuration contains 632 atoms in 212 residues
31: [ OK ] InsertMoleculesTest.InsertsMoleculesWithReplacement (73 ms)
31: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions
31: Initialising inter-atomic distances...
31:
31: WARNING: Masses and atomic (Van der Waals) radii will be guessed
31: based on residue and atom names, since they could not be
31: definitively assigned from the information in your input
31: files. These guessed numbers might deviate from the mass
31: and radius of the atom type. Please check the output
31: files if necessary.
31:
31: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
31: from the source below. This means the results may be different
31: compared to previous GROMACS versions.
31:
31: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
31: A. Bondi
31: van der Waals Volumes and Radii
31: J. Phys. Chem. 68 (1964) pp. 441-451
31: -------- -------- --- Thank You --- -------- --------
31:
31: Using random seed 1997
31: Read 4 positions from file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_5.dat
31:
31:
Try 1 success (now 2 atoms)!
31:
Try 2 success (now 4 atoms)!
31:
Try 3
Try 4
Try 5
Try 6
Try 7
Try 8
Try 9
Try 10
Try 11
Try 12 skipped position (0.990, 2.010, 3.000)
31:
Try 13 success (now 6 atoms)!
31:
31: Added 3 molecules (out of 4 requested)
31: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_out.gro
31:
31: Output configuration contains 6 atoms in 3 residues
31: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions (12 ms)
31: [----------] 5 tests from InsertMoleculesTest (142 ms total)
31:
31: [----------] 14 tests from GetIrTest
31: [ RUN ] GetIrTest.HandlesDifferentKindsOfMdpLines
31: Ignoring obsolete mdp entry 'title'
31: Replacing old mdp entry 'xtc_grps' by 'compressed-x-grps'
31:
31: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_HandlesDifferentKindsOfMdpLines_input.mdp]:
31: For a correct single-point energy evaluation with nsteps = 0, use
31: continuation = yes to avoid constraining the input coordinates.
31:
31: [ OK ] GetIrTest.HandlesDifferentKindsOfMdpLines (27 ms)
31: [ RUN ] GetIrTest.RejectsNonCommentLineWithNoEquals
31: [ OK ] GetIrTest.RejectsNonCommentLineWithNoEquals (30 ms)
31: [ RUN ] GetIrTest.AcceptsKeyWithoutValue
31:
31: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsKeyWithoutValue_input.mdp]:
31: For a correct single-point energy evaluation with nsteps = 0, use
31: continuation = yes to avoid constraining the input coordinates.
31:
31: [ OK ] GetIrTest.AcceptsKeyWithoutValue (42 ms)
31: [ RUN ] GetIrTest.RejectsValueWithoutKey
31: [ OK ] GetIrTest.RejectsValueWithoutKey (29 ms)
31: [ RUN ] GetIrTest.RejectsEmptyKeyAndEmptyValue
31: [ OK ] GetIrTest.RejectsEmptyKeyAndEmptyValue (29 ms)
31: [ RUN ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment
31:
31: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsDefineParametersWithValuesIncludingAssignment_input.mdp]:
31: For a correct single-point energy evaluation with nsteps = 0, use
31: continuation = yes to avoid constraining the input coordinates.
31:
31: [ OK ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment (19 ms)
31: [ RUN ] GetIrTest.AcceptsEmptyLines
31:
31: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsEmptyLines_input.mdp]:
31: For a correct single-point energy evaluation with nsteps = 0, use
31: continuation = yes to avoid constraining the input coordinates.
31:
31: [ OK ] GetIrTest.AcceptsEmptyLines (18 ms)
31: [ RUN ] GetIrTest.AcceptsElectricField
31:
31: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricField_input.mdp]:
31: For a correct single-point energy evaluation with nsteps = 0, use
31: continuation = yes to avoid constraining the input coordinates.
31:
31: [ OK ] GetIrTest.AcceptsElectricField (18 ms)
31: [ RUN ] GetIrTest.AcceptsElectricFieldPulsed
31:
31: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldPulsed_input.mdp]:
31: For a correct single-point energy evaluation with nsteps = 0, use
31: continuation = yes to avoid constraining the input coordinates.
31:
31: [ OK ] GetIrTest.AcceptsElectricFieldPulsed (26 ms)
31: [ RUN ] GetIrTest.AcceptsElectricFieldOscillating
31:
31: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldOscillating_input.mdp]:
31: For a correct single-point energy evaluation with nsteps = 0, use
31: continuation = yes to avoid constraining the input coordinates.
31:
31: [ OK ] GetIrTest.AcceptsElectricFieldOscillating (46 ms)
31: [ RUN ] GetIrTest.RejectsDuplicateOldAndNewKeys
31: [ OK ] GetIrTest.RejectsDuplicateOldAndNewKeys (13 ms)
31: [ RUN ] GetIrTest.AcceptsImplicitSolventNo
31:
31: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsImplicitSolventNo_input.mdp]:
31: For a correct single-point energy evaluation with nsteps = 0, use
31: continuation = yes to avoid constraining the input coordinates.
31:
31: [ OK ] GetIrTest.AcceptsImplicitSolventNo (22 ms)
31: [ RUN ] GetIrTest.RejectsImplicitSolventYes
31: [ OK ] GetIrTest.RejectsImplicitSolventYes (29 ms)
31: [ RUN ] GetIrTest.AcceptsMimic
31:
31: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsMimic_input.mdp]:
31: For a correct single-point energy evaluation with nsteps = 0, use
31: continuation = yes to avoid constraining the input coordinates.
31:
31: [ OK ] GetIrTest.AcceptsMimic (28 ms)
31: [----------] 14 tests from GetIrTest (379 ms total)
31:
31: [----------] 5 tests from SolvateTest
31: [ RUN ] SolvateTest.cs_box_Works
31: Reading solvent configuration
31:
31: Initialising inter-atomic distances...
31:
31: WARNING: Masses and atomic (Van der Waals) radii will be guessed
31: based on residue and atom names, since they could not be
31: definitively assigned from the information in your input
31: files. These guessed numbers might deviate from the mass
31: and radius of the atom type. Please check the output
31: files if necessary.
31:
31: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
31: from the source below. This means the results may be different
31: compared to previous GROMACS versions.
31:
31: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
31: A. Bondi
31: van der Waals Volumes and Radii
31: J. Phys. Chem. 68 (1964) pp. 441-451
31: -------- -------- --- Thank You --- -------- --------
31:
31: Generating solvent configuration
31: Will generate new solvent configuration of 1x1x1 boxes
31: Solvent box contains 270 atoms in 90 residues
31: Removed 129 solvent atoms due to solvent-solvent overlap
31: Sorting configuration
31: Found 1 molecule type:
31: SOL ( 3 atoms): 47 residues
31: Generated solvent containing 141 atoms in 47 residues
31: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_box_Works_out.gro
31:
31: Output configuration contains 141 atoms in 47 residues
31: Volume : 1.331 (nm^3)
31: Density : 1056.36 (g/l)
31: Number of solvent molecules: 47
31:
31: [ OK ] SolvateTest.cs_box_Works (96 ms)
31: [ RUN ] SolvateTest.cs_cp_Works
31: Reading solute configuration
31: Reading solvent configuration
31:
31: Initialising inter-atomic distances...
31:
31: WARNING: Masses and atomic (Van der Waals) radii will be guessed
31: based on residue and atom names, since they could not be
31: definitively assigned from the information in your input
31: files. These guessed numbers might deviate from the mass
31: and radius of the atom type. Please check the output
31: files if necessary.
31:
31: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
31: from the source below. This means the results may be different
31: compared to previous GROMACS versions.
31:
31: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
31: A. Bondi
31: van der Waals Volumes and Radii
31: J. Phys. Chem. 68 (1964) pp. 441-451
31: -------- -------- --- Thank You --- -------- --------
31:
31: Generating solvent configuration
31: Will generate new solvent configuration of 2x2x2 boxes
31: Solvent box contains 3660 atoms in 1220 residues
31: Removed 987 solvent atoms due to solvent-solvent overlap
31: Removed 15 solvent atoms due to solute-solvent overlap
31: Sorting configuration
31: Found 1 molecule type:
31: SOL ( 3 atoms): 886 residues
31: Generated solvent containing 2658 atoms in 886 residues
31: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_Works_out.gro
31:
31: Output configuration contains 2664 atoms in 888 residues
31: Volume : 27.2709 (nm^3)
31: Density : 974.777 (g/l)
31: Number of solvent molecules: 886
31:
31: [ OK ] SolvateTest.cs_cp_Works (275 ms)
31: [ RUN ] SolvateTest.cs_cp_p_Works
31: Reading solute configuration
31: Reading solvent configuration
31:
31: Initialising inter-atomic distances...
31:
31: WARNING: Masses and atomic (Van der Waals) radii will be guessed
31: based on residue and atom names, since they could not be
31: definitively assigned from the information in your input
31: files. These guessed numbers might deviate from the mass
31: and radius of the atom type. Please check the output
31: files if necessary.
31:
31: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
31: from the source below. This means the results may be different
31: compared to previous GROMACS versions.
31:
31: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
31: A. Bondi
31: van der Waals Volumes and Radii
31: J. Phys. Chem. 68 (1964) pp. 441-451
31: -------- -------- --- Thank You --- -------- --------
31:
31: Generating solvent configuration
31: Will generate new solvent configuration of 2x2x2 boxes
31: Solvent box contains 3660 atoms in 1220 residues
31: Removed 987 solvent atoms due to solvent-solvent overlap
31: Removed 15 solvent atoms due to solute-solvent overlap
31: Sorting configuration
31: Found 1 molecule type:
31: SOL ( 3 atoms): 886 residues
31: Generated solvent containing 2658 atoms in 886 residues
31: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_out.gro
31:
31: Output configuration contains 2664 atoms in 888 residues
31: Volume : 27.2709 (nm^3)
31: Density : 974.777 (g/l)
31: Number of solvent molecules: 886
31:
31: Processing topology
31: Adding line for 886 solvent molecules with resname (SOL) to topology file (/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_spc-and-methanol.top)
31: [ OK ] SolvateTest.cs_cp_p_Works (289 ms)
31: [ RUN ] SolvateTest.shell_Works
31: Reading solute configuration
31: Reading solvent configuration
31:
31: Initialising inter-atomic distances...
31:
31: WARNING: Masses and atomic (Van der Waals) radii will be guessed
31: based on residue and atom names, since they could not be
31: definitively assigned from the information in your input
31: files. These guessed numbers might deviate from the mass
31: and radius of the atom type. Please check the output
31: files if necessary.
31:
31: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
31: from the source below. This means the results may be different
31: compared to previous GROMACS versions.
31:
31: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
31: A. Bondi
31: van der Waals Volumes and Radii
31: J. Phys. Chem. 68 (1964) pp. 441-451
31: -------- -------- --- Thank You --- -------- --------
31:
31: Generating solvent configuration
31: Will generate new solvent configuration of 2x2x2 boxes
31: Solvent box contains 3660 atoms in 1220 residues
31: Removed 987 solvent atoms due to solvent-solvent overlap
31: Removed 1902 solvent atoms more than 1.000000 nm from solute.
31: Removed 15 solvent atoms due to solute-solvent overlap
31: Sorting configuration
31: Found 1 molecule type:
31: SOL ( 3 atoms): 252 residues
31: Generated solvent containing 756 atoms in 252 residues
31: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_shell_Works_out.gro
31:
31: Output configuration contains 762 atoms in 254 residues
31: Volume : 27.2709 (nm^3)
31: Density : 279.3 (g/l)
31: Number of solvent molecules: 252
31:
31: [ OK ] SolvateTest.shell_Works (134 ms)
31: [ RUN ] SolvateTest.update_Topology_Works
31: Reading solute configuration
31: Reading solvent configuration
31:
31: Initialising inter-atomic distances...
31:
31: WARNING: Masses and atomic (Van der Waals) radii will be guessed
31: based on residue and atom names, since they could not be
31: definitively assigned from the information in your input
31: files. These guessed numbers might deviate from the mass
31: and radius of the atom type. Please check the output
31: files if necessary.
31:
31: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
31: from the source below. This means the results may be different
31: compared to previous GROMACS versions.
31:
31: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
31: A. Bondi
31: van der Waals Volumes and Radii
31: J. Phys. Chem. 68 (1964) pp. 441-451
31: -------- -------- --- Thank You --- -------- --------
31:
31: Generating solvent configuration
31: Will generate new solvent configuration of 3x3x3 boxes
31: Solvent box contains 14952 atoms in 4984 residues
31: Removed 2787 solvent atoms due to solvent-solvent overlap
31: Removed 30 solvent atoms due to solute-solvent overlap
31: Sorting configuration
31: Found 2 different molecule types:
31: HOH ( 3 atoms): 1876 residues
31: SOL ( 3 atoms): 2169 residues
31: Generated solvent containing 0 atoms in 0 residues
31: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_out.gro
31:
31: Output configuration contains 12141 atoms in 4047 residues
31: Volume : 125 (nm^3)
31: Density : 968.963 (g/l)
31: Number of solvent molecules: 4045
31:
31: Processing topology
31: Adding line for 1876 solvent molecules with resname (HOH) to topology file (/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top)
31: Adding line for 2169 solvent molecules with resname (SOL) to topology file (/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top)
31: [ OK ] SolvateTest.update_Topology_Works (1188 ms)
31: [----------] 5 tests from SolvateTest (1984 ms total)
31:
31: [----------] 1 test from TopDirTests
31: [ RUN ] TopDirTests.NamesArrayHasCorrectSize
31: [ OK ] TopDirTests.NamesArrayHasCorrectSize (0 ms)
31: [----------] 1 test from TopDirTests (0 ms total)
31:
31: [----------] 18 tests from SinglePeptideFragments/EditconfTest
31: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/0
31: Note that major changes are planned in future for editconf, to improve usability and utility.
31: Read 252 atoms
31: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
31: No velocities found
31: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/0 (246 ms)
31: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/1
31: Note that major changes are planned in future for editconf, to improve usability and utility.
31: Read 252 atoms
31: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
31: No velocities found
31: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/1 (39 ms)
31: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/2
31: Note that major changes are planned in future for editconf, to improve usability and utility.
31: Read 252 atoms
31: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
31: No velocities found
31: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/2 (37 ms)
31: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/3
31: Note that major changes are planned in future for editconf, to improve usability and utility.
31: Read 252 atoms
31: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
31: No velocities found
31: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/3 (36 ms)
31: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/4
31: Note that major changes are planned in future for editconf, to improve usability and utility.
31: Read 252 atoms
31: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
31: No velocities found
31: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/4 (15 ms)
31: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/5
31: Note that major changes are planned in future for editconf, to improve usability and utility.
31: Read 252 atoms
31: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
31: No velocities found
31: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/5 (16 ms)
31: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/6
31: Note that major changes are planned in future for editconf, to improve usability and utility.
31: Read 252 atoms
31: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
31: No velocities found
31: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/6 (43 ms)
31: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/7
31: Note that major changes are planned in future for editconf, to improve usability and utility.
31: Read 252 atoms
31: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
31: No velocities found
31: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/7 (16 ms)
31: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/8
31: Note that major changes are planned in future for editconf, to improve usability and utility.
31: Read 252 atoms
31: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
31: No velocities found
31: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/8 (18 ms)
31: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/0
31:
31: Select a group for output:
31: Group 0 ( two_residues) has 23 elements
31: There is one group in the index
31: Note that major changes are planned in future for editconf, to improve usability and utility.
31: Read 252 atoms
31: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
31: No velocities found
31: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/0 (46 ms)
31: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/1
31:
31: Select a group for output:
31: Group 0 ( two_residues) has 23 elements
31: There is one group in the index
31: Note that major changes are planned in future for editconf, to improve usability and utility.
31: Read 252 atoms
31: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
31: No velocities found
31: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/1 (32 ms)
31: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/2
31:
31: Select a group for output:
31: Group 0 ( two_residues) has 23 elements
31: There is one group in the index
31: Note that major changes are planned in future for editconf, to improve usability and utility.
31: Read 252 atoms
31: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
31: No velocities found
31: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/2 (36 ms)
31: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/3
31:
31: Select a group for output:
31: Group 0 ( two_residues) has 23 elements
31: There is one group in the index
31: Note that major changes are planned in future for editconf, to improve usability and utility.
31: Read 252 atoms
31: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
31: No velocities found
31: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/3 (15 ms)
31: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/4
31:
31: Select a group for output:
31: Group 0 ( two_residues) has 23 elements
31: There is one group in the index
31: Note that major changes are planned in future for editconf, to improve usability and utility.
31: Read 252 atoms
31: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
31: No velocities found
31: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/4 (12 ms)
31: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/5
31:
31: Select a group for output:
31: Group 0 ( two_residues) has 23 elements
31: There is one group in the index
31: Note that major changes are planned in future for editconf, to improve usability and utility.
31: Read 252 atoms
31: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
31: No velocities found
31: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/5 (12 ms)
31: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/6
31:
31: Select a group for output:
31: Group 0 ( two_residues) has 23 elements
31: There is one group in the index
31: Note that major changes are planned in future for editconf, to improve usability and utility.
31: Read 252 atoms
31: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
31: No velocities found
31: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/6 (17 ms)
31: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/7
31:
31: Select a group for output:
31: Group 0 ( two_residues) has 23 elements
31: There is one group in the index
31: Note that major changes are planned in future for editconf, to improve usability and utility.
31: Read 252 atoms
31: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
31: No velocities found
31: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/7 (13 ms)
31: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/8
31:
31: Select a group for output:
31: Group 0 ( two_residues) has 23 elements
31: There is one group in the index
31: Note that major changes are planned in future for editconf, to improve usability and utility.
31: Read 252 atoms
31: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
31: No velocities found
31: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/8 (14 ms)
31: [----------] 18 tests from SinglePeptideFragments/EditconfTest (663 ms total)
31:
31: [----------] Global test environment tear-down
31: [==========] 69 tests from 10 test cases ran. (9593 ms total)
31: [ PASSED ] 69 tests.
31/52 Test #31: GmxPreprocessTests .................. Passed 9.67 sec
test 32
Start 32: Pdb2gmx1Test
32: Test command: /<<PKGBUILDDIR>>/build/basic/bin/pdb2gmx1-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/Pdb2gmx1Test.xml"
32: Test timeout computed to be: 30
32: [==========] Running 24 tests from 1 test case.
32: [----------] Global test environment set-up.
32: [----------] 24 tests from ForOplsaa/Pdb2gmxTest
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/0
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 25 donors and 23 acceptors were found.
32: There are 41 hydrogen bonds
32: Will use HISE for residue 8
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS3 HIS8
32: SG9 NE251
32: HIS8 NE251 1.055
32: MET12 SD83 0.763 0.990
32: Making bonds...
32: Number of bonds was 254, now 254
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 653 pairs
32: Before cleaning: 663 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 663 dihedrals, 51 impropers, 457 angles
32: 650 pairs, 254 bonds and 0 virtual sites
32: Total mass 1846.112 a.m.u.
32: Total charge -0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 128
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (128 atoms, 16 residues)
32: Identified residue ALA2 as a starting terminus.
32: Identified residue SER17 as a ending terminus.
32: Start terminus ALA-2: NH3+
32: End terminus SER-17: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 252 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
32: The Oplsaa force field and the tip3p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/0 (583 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/1
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 30 donors and 22 acceptors were found.
32: There are 36 hydrogen bonds
32: Will use HISE for residue 29
32: Will use HISE for residue 32
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS27 HIS29
32: SG90 NE2111
32: HIS29 NE2111 0.987
32: HIS32 NE2135 1.590 1.155
32: Making bonds...
32: Number of bonds was 290, now 290
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 748 pairs
32: Before cleaning: 778 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 778 dihedrals, 72 impropers, 516 angles
32: 736 pairs, 290 bonds and 0 virtual sites
32: Total mass 2088.357 a.m.u.
32: Total charge 1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 149
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (149 atoms, 16 residues)
32: Identified residue THR18 as a starting terminus.
32: Identified residue PHE33 as a ending terminus.
32: Start terminus THR-18: NH3+
32: End terminus PHE-33: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 281 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
32: The Oplsaa force field and the tip3p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/1 (578 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/2
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 22 acceptors were found.
32: There are 26 hydrogen bonds
32: Will use HISE for residue 45
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS45
32: NE295
32: MET46 SD102 1.078
32: Making bonds...
32: Number of bonds was 261, now 261
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 676 pairs
32: Before cleaning: 696 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 696 dihedrals, 56 impropers, 472 angles
32: 667 pairs, 261 bonds and 0 virtual sites
32: Total mass 1861.128 a.m.u.
32: Total charge -1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 132
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (132 atoms, 16 residues)
32: Identified residue ALA34 as a starting terminus.
32: Identified residue ALA49 as a ending terminus.
32: Start terminus ALA-34: NH3+
32: End terminus ALA-49: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 255 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
32: The Oplsaa force field and the tip3p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/2 (516 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/3
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 21 acceptors were found.
32: There are 30 hydrogen bonds
32: Will use HISE for residue 60
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS60
32: NE285
32: CYS62 SG98 0.803
32: Making bonds...
32: Number of bonds was 232, now 232
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 603 pairs
32: Before cleaning: 618 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 618 dihedrals, 48 impropers, 419 angles
32: 597 pairs, 232 bonds and 0 virtual sites
32: Total mass 1662.883 a.m.u.
32: Total charge -0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 117
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (117 atoms, 16 residues)
32: Identified residue LYS50 as a starting terminus.
32: Identified residue PRO65 as a ending terminus.
32: Start terminus LYS-50: NH3+
32: End terminus PRO-65: PRO-COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 228 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
32: The Oplsaa force field and the tip3p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/3 (487 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/4
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 25 donors and 23 acceptors were found.
32: There are 41 hydrogen bonds
32: Will use HISE for residue 8
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS3 HIS8
32: SG9 NE251
32: HIS8 NE251 1.055
32: MET12 SD83 0.763 0.990
32: Making bonds...
32: Number of bonds was 254, now 254
32: Marked 124 virtual sites
32: Added 16 dummy masses
32: Added 26 new constraints
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 653 pairs
32: Before cleaning: 663 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 663 dihedrals, 51 impropers, 457 angles
32: 650 pairs, 254 bonds and 130 virtual sites
32: Total mass 1846.112 a.m.u.
32: Total charge -0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 128
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (128 atoms, 16 residues)
32: Identified residue ALA2 as a starting terminus.
32: Identified residue SER17 as a ending terminus.
32: Start terminus ALA-2: NH3+
32: End terminus SER-17: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 252 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
32: The Oplsaa force field and the tip3p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/4 (558 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/5
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 30 donors and 22 acceptors were found.
32: There are 36 hydrogen bonds
32: Will use HISE for residue 29
32: Will use HISE for residue 32
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS27 HIS29
32: SG90 NE2111
32: HIS29 NE2111 0.987
32: HIS32 NE2135 1.590 1.155
32: Making bonds...
32: Number of bonds was 290, now 290
32: Marked 132 virtual sites
32: Added 10 dummy masses
32: Added 19 new constraints
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 748 pairs
32: Before cleaning: 778 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 778 dihedrals, 72 impropers, 516 angles
32: 736 pairs, 290 bonds and 133 virtual sites
32: Total mass 2088.357 a.m.u.
32: Total charge 1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 149
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (149 atoms, 16 residues)
32: Identified residue THR18 as a starting terminus.
32: Identified residue PHE33 as a ending terminus.
32: Start terminus THR-18: NH3+
32: End terminus PHE-33: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 281 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
32: The Oplsaa force field and the tip3p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/5 (601 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/6
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 22 acceptors were found.
32: There are 26 hydrogen bonds
32: Will use HISE for residue 45
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS45
32: NE295
32: MET46 SD102 1.078
32: Making bonds...
32: Number of bonds was 261, now 261
32: Marked 123 virtual sites
32: Added 22 dummy masses
32: Added 35 new constraints
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 676 pairs
32: Before cleaning: 696 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 696 dihedrals, 56 impropers, 472 angles
32: 667 pairs, 261 bonds and 132 virtual sites
32: Total mass 1861.128 a.m.u.
32: Total charge -1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 132
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (132 atoms, 16 residues)
32: Identified residue ALA34 as a starting terminus.
32: Identified residue ALA49 as a ending terminus.
32: Start terminus ALA-34: NH3+
32: End terminus ALA-49: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 255 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
32: The Oplsaa force field and the tip3p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/6 (563 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/7
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 21 acceptors were found.
32: There are 30 hydrogen bonds
32: Will use HISE for residue 60
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS60
32: NE285
32: CYS62 SG98 0.803
32: Making bonds...
32: Number of bonds was 232, now 232
32: Marked 111 virtual sites
32: Added 18 dummy masses
32: Added 31 new constraints
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 603 pairs
32: Before cleaning: 618 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 618 dihedrals, 48 impropers, 419 angles
32: 597 pairs, 232 bonds and 116 virtual sites
32: Total mass 1662.883 a.m.u.
32: Total charge -0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 117
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (117 atoms, 16 residues)
32: Identified residue LYS50 as a starting terminus.
32: Identified residue PRO65 as a ending terminus.
32: Start terminus LYS-50: NH3+
32: End terminus PRO-65: PRO-COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 228 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
32: The Oplsaa force field and the tip3p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/7 (505 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/8
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 25 donors and 23 acceptors were found.
32: There are 41 hydrogen bonds
32: Will use HISE for residue 8
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS3 HIS8
32: SG9 NE251
32: HIS8 NE251 1.055
32: MET12 SD83 0.763 0.990
32: Making bonds...
32: Number of bonds was 254, now 254
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 653 pairs
32: Before cleaning: 663 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 663 dihedrals, 51 impropers, 457 angles
32: 650 pairs, 254 bonds and 0 virtual sites
32: Total mass 1846.112 a.m.u.
32: Total charge -0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 128
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (128 atoms, 16 residues)
32: Identified residue ALA2 as a starting terminus.
32: Identified residue SER17 as a ending terminus.
32: Start terminus ALA-2: NH3+
32: End terminus SER-17: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 252 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
32: The Oplsaa force field and the tip4p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/8 (508 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/9
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 30 donors and 22 acceptors were found.
32: There are 36 hydrogen bonds
32: Will use HISE for residue 29
32: Will use HISE for residue 32
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS27 HIS29
32: SG90 NE2111
32: HIS29 NE2111 0.987
32: HIS32 NE2135 1.590 1.155
32: Making bonds...
32: Number of bonds was 290, now 290
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 748 pairs
32: Before cleaning: 778 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 778 dihedrals, 72 impropers, 516 angles
32: 736 pairs, 290 bonds and 0 virtual sites
32: Total mass 2088.357 a.m.u.
32: Total charge 1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 149
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (149 atoms, 16 residues)
32: Identified residue THR18 as a starting terminus.
32: Identified residue PHE33 as a ending terminus.
32: Start terminus THR-18: NH3+
32: End terminus PHE-33: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 281 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
32: The Oplsaa force field and the tip4p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/9 (563 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/10
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 22 acceptors were found.
32: There are 26 hydrogen bonds
32: Will use HISE for residue 45
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS45
32: NE295
32: MET46 SD102 1.078
32: Making bonds...
32: Number of bonds was 261, now 261
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 676 pairs
32: Before cleaning: 696 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 696 dihedrals, 56 impropers, 472 angles
32: 667 pairs, 261 bonds and 0 virtual sites
32: Total mass 1861.128 a.m.u.
32: Total charge -1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 132
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (132 atoms, 16 residues)
32: Identified residue ALA34 as a starting terminus.
32: Identified residue ALA49 as a ending terminus.
32: Start terminus ALA-34: NH3+
32: End terminus ALA-49: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 255 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
32: The Oplsaa force field and the tip4p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/10 (520 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/11
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 21 acceptors were found.
32: There are 30 hydrogen bonds
32: Will use HISE for residue 60
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS60
32: NE285
32: CYS62 SG98 0.803
32: Making bonds...
32: Number of bonds was 232, now 232
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 603 pairs
32: Before cleaning: 618 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 618 dihedrals, 48 impropers, 419 angles
32: 597 pairs, 232 bonds and 0 virtual sites
32: Total mass 1662.883 a.m.u.
32: Total charge -0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 117
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (117 atoms, 16 residues)
32: Identified residue LYS50 as a starting terminus.
32: Identified residue PRO65 as a ending terminus.
32: Start terminus LYS-50: NH3+
32: End terminus PRO-65: PRO-COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 228 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
32: The Oplsaa force field and the tip4p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/11 (469 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/12
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 25 donors and 23 acceptors were found.
32: There are 41 hydrogen bonds
32: Will use HISE for residue 8
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS3 HIS8
32: SG9 NE251
32: HIS8 NE251 1.055
32: MET12 SD83 0.763 0.990
32: Making bonds...
32: Number of bonds was 254, now 254
32: Marked 124 virtual sites
32: Added 16 dummy masses
32: Added 26 new constraints
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 653 pairs
32: Before cleaning: 663 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 663 dihedrals, 51 impropers, 457 angles
32: 650 pairs, 254 bonds and 130 virtual sites
32: Total mass 1846.112 a.m.u.
32: Total charge -0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 128
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (128 atoms, 16 residues)
32: Identified residue ALA2 as a starting terminus.
32: Identified residue SER17 as a ending terminus.
32: Start terminus ALA-2: NH3+
32: End terminus SER-17: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 252 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
32: The Oplsaa force field and the tip4p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/12 (538 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/13
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 30 donors and 22 acceptors were found.
32: There are 36 hydrogen bonds
32: Will use HISE for residue 29
32: Will use HISE for residue 32
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS27 HIS29
32: SG90 NE2111
32: HIS29 NE2111 0.987
32: HIS32 NE2135 1.590 1.155
32: Making bonds...
32: Number of bonds was 290, now 290
32: Marked 132 virtual sites
32: Added 10 dummy masses
32: Added 19 new constraints
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 748 pairs
32: Before cleaning: 778 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 778 dihedrals, 72 impropers, 516 angles
32: 736 pairs, 290 bonds and 133 virtual sites
32: Total mass 2088.357 a.m.u.
32: Total charge 1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 149
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (149 atoms, 16 residues)
32: Identified residue THR18 as a starting terminus.
32: Identified residue PHE33 as a ending terminus.
32: Start terminus THR-18: NH3+
32: End terminus PHE-33: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 281 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
32: The Oplsaa force field and the tip4p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/13 (606 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/14
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 22 acceptors were found.
32: There are 26 hydrogen bonds
32: Will use HISE for residue 45
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS45
32: NE295
32: MET46 SD102 1.078
32: Making bonds...
32: Number of bonds was 261, now 261
32: Marked 123 virtual sites
32: Added 22 dummy masses
32: Added 35 new constraints
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 676 pairs
32: Before cleaning: 696 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 696 dihedrals, 56 impropers, 472 angles
32: 667 pairs, 261 bonds and 132 virtual sites
32: Total mass 1861.128 a.m.u.
32: Total charge -1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 132
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (132 atoms, 16 residues)
32: Identified residue ALA34 as a starting terminus.
32: Identified residue ALA49 as a ending terminus.
32: Start terminus ALA-34: NH3+
32: End terminus ALA-49: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 255 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
32: The Oplsaa force field and the tip4p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/14 (569 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/15
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 21 acceptors were found.
32: There are 30 hydrogen bonds
32: Will use HISE for residue 60
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS60
32: NE285
32: CYS62 SG98 0.803
32: Making bonds...
32: Number of bonds was 232, now 232
32: Marked 111 virtual sites
32: Added 18 dummy masses
32: Added 31 new constraints
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 603 pairs
32: Before cleaning: 618 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 618 dihedrals, 48 impropers, 419 angles
32: 597 pairs, 232 bonds and 116 virtual sites
32: Total mass 1662.883 a.m.u.
32: Total charge -0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 117
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (117 atoms, 16 residues)
32: Identified residue LYS50 as a starting terminus.
32: Identified residue PRO65 as a ending terminus.
32: Start terminus LYS-50: NH3+
32: End terminus PRO-65: PRO-COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 228 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
32: The Oplsaa force field and the tip4p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/15 (517 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/16
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 25 donors and 23 acceptors were found.
32: There are 41 hydrogen bonds
32: Will use HISE for residue 8
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS3 HIS8
32: SG9 NE251
32: HIS8 NE251 1.055
32: MET12 SD83 0.763 0.990
32: Making bonds...
32: Number of bonds was 254, now 254
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 653 pairs
32: Before cleaning: 663 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 663 dihedrals, 51 impropers, 457 angles
32: 650 pairs, 254 bonds and 0 virtual sites
32: Total mass 1846.112 a.m.u.
32: Total charge -0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 128
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (128 atoms, 16 residues)
32: Identified residue ALA2 as a starting terminus.
32: Identified residue SER17 as a ending terminus.
32: Start terminus ALA-2: NH3+
32: End terminus SER-17: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 252 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
32: The Oplsaa force field and the tip5p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/16 (503 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/17
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 30 donors and 22 acceptors were found.
32: There are 36 hydrogen bonds
32: Will use HISE for residue 29
32: Will use HISE for residue 32
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS27 HIS29
32: SG90 NE2111
32: HIS29 NE2111 0.987
32: HIS32 NE2135 1.590 1.155
32: Making bonds...
32: Number of bonds was 290, now 290
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 748 pairs
32: Before cleaning: 778 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 778 dihedrals, 72 impropers, 516 angles
32: 736 pairs, 290 bonds and 0 virtual sites
32: Total mass 2088.357 a.m.u.
32: Total charge 1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 149
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (149 atoms, 16 residues)
32: Identified residue THR18 as a starting terminus.
32: Identified residue PHE33 as a ending terminus.
32: Start terminus THR-18: NH3+
32: End terminus PHE-33: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 281 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
32: The Oplsaa force field and the tip5p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/17 (574 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/18
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 22 acceptors were found.
32: There are 26 hydrogen bonds
32: Will use HISE for residue 45
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS45
32: NE295
32: MET46 SD102 1.078
32: Making bonds...
32: Number of bonds was 261, now 261
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 676 pairs
32: Before cleaning: 696 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 696 dihedrals, 56 impropers, 472 angles
32: 667 pairs, 261 bonds and 0 virtual sites
32: Total mass 1861.128 a.m.u.
32: Total charge -1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 132
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (132 atoms, 16 residues)
32: Identified residue ALA34 as a starting terminus.
32: Identified residue ALA49 as a ending terminus.
32: Start terminus ALA-34: NH3+
32: End terminus ALA-49: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 255 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
32: The Oplsaa force field and the tip5p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/18 (532 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/19
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 21 acceptors were found.
32: There are 30 hydrogen bonds
32: Will use HISE for residue 60
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS60
32: NE285
32: CYS62 SG98 0.803
32: Making bonds...
32: Number of bonds was 232, now 232
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 603 pairs
32: Before cleaning: 618 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 618 dihedrals, 48 impropers, 419 angles
32: 597 pairs, 232 bonds and 0 virtual sites
32: Total mass 1662.883 a.m.u.
32: Total charge -0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 117
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (117 atoms, 16 residues)
32: Identified residue LYS50 as a starting terminus.
32: Identified residue PRO65 as a ending terminus.
32: Start terminus LYS-50: NH3+
32: End terminus PRO-65: PRO-COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 228 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
32: The Oplsaa force field and the tip5p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/19 (480 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/20
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 25 donors and 23 acceptors were found.
32: There are 41 hydrogen bonds
32: Will use HISE for residue 8
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS3 HIS8
32: SG9 NE251
32: HIS8 NE251 1.055
32: MET12 SD83 0.763 0.990
32: Making bonds...
32: Number of bonds was 254, now 254
32: Marked 124 virtual sites
32: Added 16 dummy masses
32: Added 26 new constraints
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 653 pairs
32: Before cleaning: 663 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 663 dihedrals, 51 impropers, 457 angles
32: 650 pairs, 254 bonds and 130 virtual sites
32: Total mass 1846.112 a.m.u.
32: Total charge -0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 128
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (128 atoms, 16 residues)
32: Identified residue ALA2 as a starting terminus.
32: Identified residue SER17 as a ending terminus.
32: Start terminus ALA-2: NH3+
32: End terminus SER-17: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 252 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
32: The Oplsaa force field and the tip5p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/20 (540 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/21
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 30 donors and 22 acceptors were found.
32: There are 36 hydrogen bonds
32: Will use HISE for residue 29
32: Will use HISE for residue 32
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS27 HIS29
32: SG90 NE2111
32: HIS29 NE2111 0.987
32: HIS32 NE2135 1.590 1.155
32: Making bonds...
32: Number of bonds was 290, now 290
32: Marked 132 virtual sites
32: Added 10 dummy masses
32: Added 19 new constraints
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 748 pairs
32: Before cleaning: 778 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 778 dihedrals, 72 impropers, 516 angles
32: 736 pairs, 290 bonds and 133 virtual sites
32: Total mass 2088.357 a.m.u.
32: Total charge 1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 149
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (149 atoms, 16 residues)
32: Identified residue THR18 as a starting terminus.
32: Identified residue PHE33 as a ending terminus.
32: Start terminus THR-18: NH3+
32: End terminus PHE-33: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 281 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
32: The Oplsaa force field and the tip5p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/21 (593 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/22
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 22 acceptors were found.
32: There are 26 hydrogen bonds
32: Will use HISE for residue 45
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS45
32: NE295
32: MET46 SD102 1.078
32: Making bonds...
32: Number of bonds was 261, now 261
32: Marked 123 virtual sites
32: Added 22 dummy masses
32: Added 35 new constraints
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 676 pairs
32: Before cleaning: 696 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 696 dihedrals, 56 impropers, 472 angles
32: 667 pairs, 261 bonds and 132 virtual sites
32: Total mass 1861.128 a.m.u.
32: Total charge -1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 132
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (132 atoms, 16 residues)
32: Identified residue ALA34 as a starting terminus.
32: Identified residue ALA49 as a ending terminus.
32: Start terminus ALA-34: NH3+
32: End terminus ALA-49: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 255 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
32: The Oplsaa force field and the tip5p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/22 (569 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/23
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 21 acceptors were found.
32: There are 30 hydrogen bonds
32: Will use HISE for residue 60
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS60
32: NE285
32: CYS62 SG98 0.803
32: Making bonds...
32: Number of bonds was 232, now 232
32: Marked 111 virtual sites
32: Added 18 dummy masses
32: Added 31 new constraints
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 603 pairs
32: Before cleaning: 618 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 618 dihedrals, 48 impropers, 419 angles
32: 597 pairs, 232 bonds and 116 virtual sites
32: Total mass 1662.883 a.m.u.
32: Total charge -0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 117
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (117 atoms, 16 residues)
32: Identified residue LYS50 as a starting terminus.
32: Identified residue PRO65 as a ending terminus.
32: Start terminus LYS-50: NH3+
32: End terminus PRO-65: PRO-COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 228 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
32: The Oplsaa force field and the tip5p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/23 (507 ms)
32: [----------] 24 tests from ForOplsaa/Pdb2gmxTest (12986 ms total)
32:
32: [----------] Global test environment tear-down
32: [==========] 24 tests from 1 test case ran. (12987 ms total)
32: [ PASSED ] 24 tests.
32/52 Test #32: Pdb2gmx1Test ........................ Passed 13.05 sec
test 33
Start 33: Pdb2gmx2Test
33: Test command: /<<PKGBUILDDIR>>/build/basic/bin/pdb2gmx2-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/Pdb2gmx2Test.xml"
33: Test timeout computed to be: 30
33: [==========] Running 32 tests from 2 test cases.
33: [----------] Global test environment set-up.
33: [----------] 16 tests from ForGromos43a1/Pdb2gmxTest
33: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/0
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 25 donors and 23 acceptors were found.
33: There are 41 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33: Making bonds...
33: Number of bonds was 172, now 167
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 267 pairs
33: Before cleaning: 305 dihedrals
33: Making cmap torsions...
33: There are 90 dihedrals, 77 impropers, 241 angles
33: 267 pairs, 167 bonds and 0 virtual sites
33: Total mass 1846.116 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos43a1 force field in directory gromos43a1.ff
33:
33: going to rename gromos43a1.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 128
33:
33: Reading residue database... (Gromos43a1)
33: Processing chain 1 (128 atoms, 16 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 165 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
33: The Gromos43a1 force field and the spc water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/0 (338 ms)
33: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/1
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 30 donors and 22 acceptors were found.
33: There are 36 hydrogen bonds
33: Will use HISE for residue 29
33: Will use HISE for residue 32
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS27 HIS29
33: SG90 NE2111
33: HIS29 NE2111 0.987
33: HIS32 NE2135 1.590 1.155
33: Making bonds...
33: Number of bonds was 216, now 211
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 273 pairs
33: Before cleaning: 429 dihedrals
33: Making cmap torsions...
33: There are 93 dihedrals, 134 impropers, 316 angles
33: 273 pairs, 211 bonds and 0 virtual sites
33: Total mass 2088.361 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos43a1 force field in directory gromos43a1.ff
33:
33: going to rename gromos43a1.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
33: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 149
33:
33: Reading residue database... (Gromos43a1)
33: Processing chain 1 (149 atoms, 16 residues)
33: Identified residue THR18 as a starting terminus.
33: Identified residue PHE33 as a ending terminus.
33: Start terminus THR-18: NH3+
33: End terminus PHE-33: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 202 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
33: The Gromos43a1 force field and the spc water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/1 (355 ms)
33: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/2
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 22 acceptors were found.
33: There are 26 hydrogen bonds
33: Will use HISE for residue 45
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS45
33: NE295
33: MET46 SD102 1.078
33: Making bonds...
33: Number of bonds was 179, now 174
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 242 pairs
33: Before cleaning: 349 dihedrals
33: Making cmap torsions...
33: There are 81 dihedrals, 102 impropers, 260 angles
33: 242 pairs, 174 bonds and 0 virtual sites
33: Total mass 1861.132 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos43a1 force field in directory gromos43a1.ff
33:
33: going to rename gromos43a1.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
33: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 132
33:
33: Reading residue database... (Gromos43a1)
33: Processing chain 1 (132 atoms, 16 residues)
33: Identified residue ALA34 as a starting terminus.
33: Identified residue ALA49 as a ending terminus.
33: Start terminus ALA-34: NH3+
33: End terminus ALA-49: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 168 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
33: The Gromos43a1 force field and the spc water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/2 (309 ms)
33: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/3
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 21 acceptors were found.
33: There are 30 hydrogen bonds
33: Will use HISE for residue 60
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS60
33: NE285
33: CYS62 SG98 0.803
33: Making bonds...
33: Number of bonds was 159, now 154
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 232 pairs
33: Before cleaning: 299 dihedrals
33: Making cmap torsions...
33: There are 78 dihedrals, 80 impropers, 227 angles
33: 232 pairs, 154 bonds and 0 virtual sites
33: Total mass 1662.887 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos43a1 force field in directory gromos43a1.ff
33:
33: going to rename gromos43a1.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
33: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 117
33:
33: Reading residue database... (Gromos43a1)
33: Processing chain 1 (117 atoms, 16 residues)
33: Identified residue LYS50 as a starting terminus.
33: Identified residue PRO65 as a ending terminus.
33: Start terminus LYS-50: NH3+
33: End terminus PRO-65: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 150 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
33: The Gromos43a1 force field and the spc water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/3 (290 ms)
33: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/4
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 25 donors and 23 acceptors were found.
33: There are 41 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33: Making bonds...
33: Number of bonds was 172, now 167
33: Marked 37 virtual sites
33: Added 4 dummy masses
33: Added 8 new constraints
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 267 pairs
33: Before cleaning: 305 dihedrals
33: Making cmap torsions...
33: There are 90 dihedrals, 77 impropers, 241 angles
33: 267 pairs, 167 bonds and 37 virtual sites
33: Total mass 1846.116 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos43a1 force field in directory gromos43a1.ff
33:
33: going to rename gromos43a1.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 128
33:
33: Reading residue database... (Gromos43a1)
33: Processing chain 1 (128 atoms, 16 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 165 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
33: The Gromos43a1 force field and the spc water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/4 (333 ms)
33: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/5
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 30 donors and 22 acceptors were found.
33: There are 36 hydrogen bonds
33: Will use HISE for residue 29
33: Will use HISE for residue 32
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS27 HIS29
33: SG90 NE2111
33: HIS29 NE2111 0.987
33: HIS32 NE2135 1.590 1.155
33: Making bonds...
33: Number of bonds was 216, now 211
33: Marked 53 virtual sites
33: Added 4 dummy masses
33: Added 10 new constraints
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 273 pairs
33: Before cleaning: 429 dihedrals
33: Making cmap torsions...
33: There are 93 dihedrals, 134 impropers, 316 angles
33: 273 pairs, 211 bonds and 51 virtual sites
33: Total mass 2088.361 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos43a1 force field in directory gromos43a1.ff
33:
33: going to rename gromos43a1.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
33: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 149
33:
33: Reading residue database... (Gromos43a1)
33: Processing chain 1 (149 atoms, 16 residues)
33: Identified residue THR18 as a starting terminus.
33: Identified residue PHE33 as a ending terminus.
33: Start terminus THR-18: NH3+
33: End terminus PHE-33: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 202 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
33: The Gromos43a1 force field and the spc water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/5 (381 ms)
33: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/6
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 22 acceptors were found.
33: There are 26 hydrogen bonds
33: Will use HISE for residue 45
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS45
33: NE295
33: MET46 SD102 1.078
33: Making bonds...
33: Number of bonds was 179, now 174
33: Marked 36 virtual sites
33: Added 4 dummy masses
33: Added 8 new constraints
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 242 pairs
33: Before cleaning: 349 dihedrals
33: Making cmap torsions...
33: There are 81 dihedrals, 102 impropers, 260 angles
33: 242 pairs, 174 bonds and 36 virtual sites
33: Total mass 1861.132 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos43a1 force field in directory gromos43a1.ff
33:
33: going to rename gromos43a1.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
33: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 132
33:
33: Reading residue database... (Gromos43a1)
33: Processing chain 1 (132 atoms, 16 residues)
33: Identified residue ALA34 as a starting terminus.
33: Identified residue ALA49 as a ending terminus.
33: Start terminus ALA-34: NH3+
33: End terminus ALA-49: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 168 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
33: The Gromos43a1 force field and the spc water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/6 (336 ms)
33: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/7
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 21 acceptors were found.
33: There are 30 hydrogen bonds
33: Will use HISE for residue 60
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS60
33: NE285
33: CYS62 SG98 0.803
33: Making bonds...
33: Number of bonds was 159, now 154
33: Marked 33 virtual sites
33: Added 4 dummy masses
33: Added 10 new constraints
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 232 pairs
33: Before cleaning: 299 dihedrals
33: Making cmap torsions...
33: There are 78 dihedrals, 80 impropers, 227 angles
33: 232 pairs, 154 bonds and 31 virtual sites
33: Total mass 1662.887 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos43a1 force field in directory gromos43a1.ff
33:
33: going to rename gromos43a1.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
33: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 117
33:
33: Reading residue database... (Gromos43a1)
33: Processing chain 1 (117 atoms, 16 residues)
33: Identified residue LYS50 as a starting terminus.
33: Identified residue PRO65 as a ending terminus.
33: Start terminus LYS-50: NH3+
33: End terminus PRO-65: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 150 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
33: The Gromos43a1 force field and the spc water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/7 (307 ms)
33: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/8
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 25 donors and 23 acceptors were found.
33: There are 41 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33: Making bonds...
33: Number of bonds was 172, now 167
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 267 pairs
33: Before cleaning: 305 dihedrals
33: Making cmap torsions...
33: There are 90 dihedrals, 77 impropers, 241 angles
33: 267 pairs, 167 bonds and 0 virtual sites
33: Total mass 1846.116 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos43a1 force field in directory gromos43a1.ff
33:
33: going to rename gromos43a1.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 128
33:
33: Reading residue database... (Gromos43a1)
33: Processing chain 1 (128 atoms, 16 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 165 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
33: The Gromos43a1 force field and the spce water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/8 (313 ms)
33: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/9
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 30 donors and 22 acceptors were found.
33: There are 36 hydrogen bonds
33: Will use HISE for residue 29
33: Will use HISE for residue 32
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS27 HIS29
33: SG90 NE2111
33: HIS29 NE2111 0.987
33: HIS32 NE2135 1.590 1.155
33: Making bonds...
33: Number of bonds was 216, now 211
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 273 pairs
33: Before cleaning: 429 dihedrals
33: Making cmap torsions...
33: There are 93 dihedrals, 134 impropers, 316 angles
33: 273 pairs, 211 bonds and 0 virtual sites
33: Total mass 2088.361 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos43a1 force field in directory gromos43a1.ff
33:
33: going to rename gromos43a1.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
33: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 149
33:
33: Reading residue database... (Gromos43a1)
33: Processing chain 1 (149 atoms, 16 residues)
33: Identified residue THR18 as a starting terminus.
33: Identified residue PHE33 as a ending terminus.
33: Start terminus THR-18: NH3+
33: End terminus PHE-33: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 202 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
33: The Gromos43a1 force field and the spce water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/9 (349 ms)
33: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/10
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 22 acceptors were found.
33: There are 26 hydrogen bonds
33: Will use HISE for residue 45
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS45
33: NE295
33: MET46 SD102 1.078
33: Making bonds...
33: Number of bonds was 179, now 174
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 242 pairs
33: Before cleaning: 349 dihedrals
33: Making cmap torsions...
33: There are 81 dihedrals, 102 impropers, 260 angles
33: 242 pairs, 174 bonds and 0 virtual sites
33: Total mass 1861.132 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos43a1 force field in directory gromos43a1.ff
33:
33: going to rename gromos43a1.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
33: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 132
33:
33: Reading residue database... (Gromos43a1)
33: Processing chain 1 (132 atoms, 16 residues)
33: Identified residue ALA34 as a starting terminus.
33: Identified residue ALA49 as a ending terminus.
33: Start terminus ALA-34: NH3+
33: End terminus ALA-49: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 168 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
33: The Gromos43a1 force field and the spce water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/10 (309 ms)
33: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/11
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 21 acceptors were found.
33: There are 30 hydrogen bonds
33: Will use HISE for residue 60
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS60
33: NE285
33: CYS62 SG98 0.803
33: Making bonds...
33: Number of bonds was 159, now 154
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 232 pairs
33: Before cleaning: 299 dihedrals
33: Making cmap torsions...
33: There are 78 dihedrals, 80 impropers, 227 angles
33: 232 pairs, 154 bonds and 0 virtual sites
33: Total mass 1662.887 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos43a1 force field in directory gromos43a1.ff
33:
33: going to rename gromos43a1.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
33: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 117
33:
33: Reading residue database... (Gromos43a1)
33: Processing chain 1 (117 atoms, 16 residues)
33: Identified residue LYS50 as a starting terminus.
33: Identified residue PRO65 as a ending terminus.
33: Start terminus LYS-50: NH3+
33: End terminus PRO-65: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 150 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
33: The Gromos43a1 force field and the spce water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/11 (289 ms)
33: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/12
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 25 donors and 23 acceptors were found.
33: There are 41 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33: Making bonds...
33: Number of bonds was 172, now 167
33: Marked 37 virtual sites
33: Added 4 dummy masses
33: Added 8 new constraints
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 267 pairs
33: Before cleaning: 305 dihedrals
33: Making cmap torsions...
33: There are 90 dihedrals, 77 impropers, 241 angles
33: 267 pairs, 167 bonds and 37 virtual sites
33: Total mass 1846.116 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos43a1 force field in directory gromos43a1.ff
33:
33: going to rename gromos43a1.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 128
33:
33: Reading residue database... (Gromos43a1)
33: Processing chain 1 (128 atoms, 16 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 165 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
33: The Gromos43a1 force field and the spce water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/12 (314 ms)
33: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/13
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 30 donors and 22 acceptors were found.
33: There are 36 hydrogen bonds
33: Will use HISE for residue 29
33: Will use HISE for residue 32
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS27 HIS29
33: SG90 NE2111
33: HIS29 NE2111 0.987
33: HIS32 NE2135 1.590 1.155
33: Making bonds...
33: Number of bonds was 216, now 211
33: Marked 53 virtual sites
33: Added 4 dummy masses
33: Added 10 new constraints
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 273 pairs
33: Before cleaning: 429 dihedrals
33: Making cmap torsions...
33: There are 93 dihedrals, 134 impropers, 316 angles
33: 273 pairs, 211 bonds and 51 virtual sites
33: Total mass 2088.361 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos43a1 force field in directory gromos43a1.ff
33:
33: going to rename gromos43a1.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
33: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 149
33:
33: Reading residue database... (Gromos43a1)
33: Processing chain 1 (149 atoms, 16 residues)
33: Identified residue THR18 as a starting terminus.
33: Identified residue PHE33 as a ending terminus.
33: Start terminus THR-18: NH3+
33: End terminus PHE-33: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 202 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
33: The Gromos43a1 force field and the spce water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/13 (374 ms)
33: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/14
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 22 acceptors were found.
33: There are 26 hydrogen bonds
33: Will use HISE for residue 45
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS45
33: NE295
33: MET46 SD102 1.078
33: Making bonds...
33: Number of bonds was 179, now 174
33: Marked 36 virtual sites
33: Added 4 dummy masses
33: Added 8 new constraints
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 242 pairs
33: Before cleaning: 349 dihedrals
33: Making cmap torsions...
33: There are 81 dihedrals, 102 impropers, 260 angles
33: 242 pairs, 174 bonds and 36 virtual sites
33: Total mass 1861.132 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos43a1 force field in directory gromos43a1.ff
33:
33: going to rename gromos43a1.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
33: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 132
33:
33: Reading residue database... (Gromos43a1)
33: Processing chain 1 (132 atoms, 16 residues)
33: Identified residue ALA34 as a starting terminus.
33: Identified residue ALA49 as a ending terminus.
33: Start terminus ALA-34: NH3+
33: End terminus ALA-49: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 168 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
33: The Gromos43a1 force field and the spce water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/14 (330 ms)
33: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/15
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 21 acceptors were found.
33: There are 30 hydrogen bonds
33: Will use HISE for residue 60
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS60
33: NE285
33: CYS62 SG98 0.803
33: Making bonds...
33: Number of bonds was 159, now 154
33: Marked 33 virtual sites
33: Added 4 dummy masses
33: Added 10 new constraints
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 232 pairs
33: Before cleaning: 299 dihedrals
33: Making cmap torsions...
33: There are 78 dihedrals, 80 impropers, 227 angles
33: 232 pairs, 154 bonds and 31 virtual sites
33: Total mass 1662.887 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos43a1 force field in directory gromos43a1.ff
33:
33: going to rename gromos43a1.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
33: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 117
33:
33: Reading residue database... (Gromos43a1)
33: Processing chain 1 (117 atoms, 16 residues)
33: Identified residue LYS50 as a starting terminus.
33: Identified residue PRO65 as a ending terminus.
33: Start terminus LYS-50: NH3+
33: End terminus PRO-65: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 150 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
33: The Gromos43a1 force field and the spce water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/15 (308 ms)
33: [----------] 16 tests from ForGromos43a1/Pdb2gmxTest (5238 ms total)
33:
33: [----------] 16 tests from ForGromos53a6/Pdb2gmxTest
33: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/0
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
33: Using default: not generating all possible dihedrals
33: Using default: excluding 3 bonded neighbors
33: Using default: generating 1,4 H--H interactions
33: Using default: removing proper dihedrals found on the same bond as a proper dihedral
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 25 donors and 23 acceptors were found.
33: There are 41 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33: Making bonds...
33: Number of bonds was 174, now 169
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 267 pairs
33: Before cleaning: 312 dihedrals
33: Making cmap torsions...
33: There are 90 dihedrals, 79 impropers, 245 angles
33: 267 pairs, 169 bonds and 0 virtual sites
33: Total mass 1846.116 a.m.u.
33: Total charge -0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos53a6 force field in directory gromos53a6.ff
33:
33: going to rename gromos53a6.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 128
33:
33: Reading residue database... (Gromos53a6)
33: Processing chain 1 (128 atoms, 16 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 167 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
33: The Gromos53a6 force field and the spc water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/0 (392 ms)
33: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/1
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
33: Using default: not generating all possible dihedrals
33: Using default: excluding 3 bonded neighbors
33: Using default: generating 1,4 H--H interactions
33: Using default: removing proper dihedrals found on the same bond as a proper dihedral
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 30 donors and 22 acceptors were found.
33: There are 36 hydrogen bonds
33: Will use HISE for residue 29
33: Will use HISE for residue 32
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS27 HIS29
33: SG90 NE2111
33: HIS29 NE2111 0.987
33: HIS32 NE2135 1.590 1.155
33: Making bonds...
33: Number of bonds was 220, now 215
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 273 pairs
33: Before cleaning: 443 dihedrals
33: Making cmap torsions...
33: There are 93 dihedrals, 138 impropers, 324 angles
33: 273 pairs, 215 bonds and 0 virtual sites
33: Total mass 2088.361 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos53a6 force field in directory gromos53a6.ff
33:
33: going to rename gromos53a6.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
33: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 149
33:
33: Reading residue database... (Gromos53a6)
33: Processing chain 1 (149 atoms, 16 residues)
33: Identified residue THR18 as a starting terminus.
33: Identified residue PHE33 as a ending terminus.
33: Start terminus THR-18: NH3+
33: End terminus PHE-33: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 206 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
33: The Gromos53a6 force field and the spc water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/1 (400 ms)
33: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/2
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
33: Using default: not generating all possible dihedrals
33: Using default: excluding 3 bonded neighbors
33: Using default: generating 1,4 H--H interactions
33: Using default: removing proper dihedrals found on the same bond as a proper dihedral
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 22 acceptors were found.
33: There are 26 hydrogen bonds
33: Will use HISE for residue 45
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS45
33: NE295
33: MET46 SD102 1.078
33: Making bonds...
33: Number of bonds was 181, now 176
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 242 pairs
33: Before cleaning: 356 dihedrals
33: Making cmap torsions...
33: There are 81 dihedrals, 104 impropers, 264 angles
33: 242 pairs, 176 bonds and 0 virtual sites
33: Total mass 1861.132 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos53a6 force field in directory gromos53a6.ff
33:
33: going to rename gromos53a6.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
33: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 132
33:
33: Reading residue database... (Gromos53a6)
33: Processing chain 1 (132 atoms, 16 residues)
33: Identified residue ALA34 as a starting terminus.
33: Identified residue ALA49 as a ending terminus.
33: Start terminus ALA-34: NH3+
33: End terminus ALA-49: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 170 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
33: The Gromos53a6 force field and the spc water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/2 (343 ms)
33: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/3
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
33: Using default: not generating all possible dihedrals
33: Using default: excluding 3 bonded neighbors
33: Using default: generating 1,4 H--H interactions
33: Using default: removing proper dihedrals found on the same bond as a proper dihedral
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 21 acceptors were found.
33: There are 30 hydrogen bonds
33: Will use HISE for residue 60
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS60
33: NE285
33: CYS62 SG98 0.803
33: Making bonds...
33: Number of bonds was 161, now 156
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 232 pairs
33: Before cleaning: 306 dihedrals
33: Making cmap torsions...
33: There are 78 dihedrals, 82 impropers, 231 angles
33: 232 pairs, 156 bonds and 0 virtual sites
33: Total mass 1662.887 a.m.u.
33: Total charge -0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos53a6 force field in directory gromos53a6.ff
33:
33: going to rename gromos53a6.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
33: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 117
33:
33: Reading residue database... (Gromos53a6)
33: Processing chain 1 (117 atoms, 16 residues)
33: Identified residue LYS50 as a starting terminus.
33: Identified residue PRO65 as a ending terminus.
33: Start terminus LYS-50: NH3+
33: End terminus PRO-65: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 152 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
33: The Gromos53a6 force field and the spc water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/3 (326 ms)
33: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/4
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
33: Using default: not generating all possible dihedrals
33: Using default: excluding 3 bonded neighbors
33: Using default: generating 1,4 H--H interactions
33: Using default: removing proper dihedrals found on the same bond as a proper dihedral
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 25 donors and 23 acceptors were found.
33: There are 41 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33: Making bonds...
33: Number of bonds was 174, now 169
33: Marked 39 virtual sites
33: Added 4 dummy masses
33: Added 8 new constraints
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 267 pairs
33: Before cleaning: 312 dihedrals
33: Making cmap torsions...
33: There are 90 dihedrals, 79 impropers, 245 angles
33: 267 pairs, 169 bonds and 39 virtual sites
33: Total mass 1846.116 a.m.u.
33: Total charge -0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos53a6 force field in directory gromos53a6.ff
33:
33: going to rename gromos53a6.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 128
33:
33: Reading residue database... (Gromos53a6)
33: Processing chain 1 (128 atoms, 16 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 167 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
33: The Gromos53a6 force field and the spc water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/4 (354 ms)
33: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/5
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
33: Using default: not generating all possible dihedrals
33: Using default: excluding 3 bonded neighbors
33: Using default: generating 1,4 H--H interactions
33: Using default: removing proper dihedrals found on the same bond as a proper dihedral
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 30 donors and 22 acceptors were found.
33: There are 36 hydrogen bonds
33: Will use HISE for residue 29
33: Will use HISE for residue 32
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS27 HIS29
33: SG90 NE2111
33: HIS29 NE2111 0.987
33: HIS32 NE2135 1.590 1.155
33: Making bonds...
33: Number of bonds was 220, now 215
33: Marked 57 virtual sites
33: Added 4 dummy masses
33: Added 10 new constraints
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 273 pairs
33: Before cleaning: 443 dihedrals
33: Making cmap torsions...
33: There are 93 dihedrals, 138 impropers, 324 angles
33: 273 pairs, 215 bonds and 55 virtual sites
33: Total mass 2088.361 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos53a6 force field in directory gromos53a6.ff
33:
33: going to rename gromos53a6.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
33: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 149
33:
33: Reading residue database... (Gromos53a6)
33: Processing chain 1 (149 atoms, 16 residues)
33: Identified residue THR18 as a starting terminus.
33: Identified residue PHE33 as a ending terminus.
33: Start terminus THR-18: NH3+
33: End terminus PHE-33: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 206 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
33: The Gromos53a6 force field and the spc water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/5 (403 ms)
33: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/6
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
33: Using default: not generating all possible dihedrals
33: Using default: excluding 3 bonded neighbors
33: Using default: generating 1,4 H--H interactions
33: Using default: removing proper dihedrals found on the same bond as a proper dihedral
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 22 acceptors were found.
33: There are 26 hydrogen bonds
33: Will use HISE for residue 45
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS45
33: NE295
33: MET46 SD102 1.078
33: Making bonds...
33: Number of bonds was 181, now 176
33: Marked 38 virtual sites
33: Added 4 dummy masses
33: Added 8 new constraints
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 242 pairs
33: Before cleaning: 356 dihedrals
33: Making cmap torsions...
33: There are 81 dihedrals, 104 impropers, 264 angles
33: 242 pairs, 176 bonds and 38 virtual sites
33: Total mass 1861.132 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos53a6 force field in directory gromos53a6.ff
33:
33: going to rename gromos53a6.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
33: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 132
33:
33: Reading residue database... (Gromos53a6)
33: Processing chain 1 (132 atoms, 16 residues)
33: Identified residue ALA34 as a starting terminus.
33: Identified residue ALA49 as a ending terminus.
33: Start terminus ALA-34: NH3+
33: End terminus ALA-49: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 170 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
33: The Gromos53a6 force field and the spc water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/6 (388 ms)
33: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/7
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
33: Using default: not generating all possible dihedrals
33: Using default: excluding 3 bonded neighbors
33: Using default: generating 1,4 H--H interactions
33: Using default: removing proper dihedrals found on the same bond as a proper dihedral
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 21 acceptors were found.
33: There are 30 hydrogen bonds
33: Will use HISE for residue 60
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS60
33: NE285
33: CYS62 SG98 0.803
33: Making bonds...
33: Number of bonds was 161, now 156
33: Marked 35 virtual sites
33: Added 4 dummy masses
33: Added 10 new constraints
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 232 pairs
33: Before cleaning: 306 dihedrals
33: Making cmap torsions...
33: There are 78 dihedrals, 82 impropers, 231 angles
33: 232 pairs, 156 bonds and 33 virtual sites
33: Total mass 1662.887 a.m.u.
33: Total charge -0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos53a6 force field in directory gromos53a6.ff
33:
33: going to rename gromos53a6.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
33: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 117
33:
33: Reading residue database... (Gromos53a6)
33: Processing chain 1 (117 atoms, 16 residues)
33: Identified residue LYS50 as a starting terminus.
33: Identified residue PRO65 as a ending terminus.
33: Start terminus LYS-50: NH3+
33: End terminus PRO-65: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 152 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
33: The Gromos53a6 force field and the spc water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/7 (333 ms)
33: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/8
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
33: Using default: not generating all possible dihedrals
33: Using default: excluding 3 bonded neighbors
33: Using default: generating 1,4 H--H interactions
33: Using default: removing proper dihedrals found on the same bond as a proper dihedral
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 25 donors and 23 acceptors were found.
33: There are 41 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33: Making bonds...
33: Number of bonds was 174, now 169
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 267 pairs
33: Before cleaning: 312 dihedrals
33: Making cmap torsions...
33: There are 90 dihedrals, 79 impropers, 245 angles
33: 267 pairs, 169 bonds and 0 virtual sites
33: Total mass 1846.116 a.m.u.
33: Total charge -0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos53a6 force field in directory gromos53a6.ff
33:
33: going to rename gromos53a6.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 128
33:
33: Reading residue database... (Gromos53a6)
33: Processing chain 1 (128 atoms, 16 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 167 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
33: The Gromos53a6 force field and the spce water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/8 (343 ms)
33: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/9
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
33: Using default: not generating all possible dihedrals
33: Using default: excluding 3 bonded neighbors
33: Using default: generating 1,4 H--H interactions
33: Using default: removing proper dihedrals found on the same bond as a proper dihedral
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 30 donors and 22 acceptors were found.
33: There are 36 hydrogen bonds
33: Will use HISE for residue 29
33: Will use HISE for residue 32
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS27 HIS29
33: SG90 NE2111
33: HIS29 NE2111 0.987
33: HIS32 NE2135 1.590 1.155
33: Making bonds...
33: Number of bonds was 220, now 215
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 273 pairs
33: Before cleaning: 443 dihedrals
33: Making cmap torsions...
33: There are 93 dihedrals, 138 impropers, 324 angles
33: 273 pairs, 215 bonds and 0 virtual sites
33: Total mass 2088.361 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos53a6 force field in directory gromos53a6.ff
33:
33: going to rename gromos53a6.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
33: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 149
33:
33: Reading residue database... (Gromos53a6)
33: Processing chain 1 (149 atoms, 16 residues)
33: Identified residue THR18 as a starting terminus.
33: Identified residue PHE33 as a ending terminus.
33: Start terminus THR-18: NH3+
33: End terminus PHE-33: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 206 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
33: The Gromos53a6 force field and the spce water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/9 (390 ms)
33: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/10
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
33: Using default: not generating all possible dihedrals
33: Using default: excluding 3 bonded neighbors
33: Using default: generating 1,4 H--H interactions
33: Using default: removing proper dihedrals found on the same bond as a proper dihedral
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 22 acceptors were found.
33: There are 26 hydrogen bonds
33: Will use HISE for residue 45
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS45
33: NE295
33: MET46 SD102 1.078
33: Making bonds...
33: Number of bonds was 181, now 176
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 242 pairs
33: Before cleaning: 356 dihedrals
33: Making cmap torsions...
33: There are 81 dihedrals, 104 impropers, 264 angles
33: 242 pairs, 176 bonds and 0 virtual sites
33: Total mass 1861.132 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos53a6 force field in directory gromos53a6.ff
33:
33: going to rename gromos53a6.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
33: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 132
33:
33: Reading residue database... (Gromos53a6)
33: Processing chain 1 (132 atoms, 16 residues)
33: Identified residue ALA34 as a starting terminus.
33: Identified residue ALA49 as a ending terminus.
33: Start terminus ALA-34: NH3+
33: End terminus ALA-49: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 170 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
33: The Gromos53a6 force field and the spce water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/10 (340 ms)
33: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/11
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
33: Using default: not generating all possible dihedrals
33: Using default: excluding 3 bonded neighbors
33: Using default: generating 1,4 H--H interactions
33: Using default: removing proper dihedrals found on the same bond as a proper dihedral
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 21 acceptors were found.
33: There are 30 hydrogen bonds
33: Will use HISE for residue 60
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS60
33: NE285
33: CYS62 SG98 0.803
33: Making bonds...
33: Number of bonds was 161, now 156
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 232 pairs
33: Before cleaning: 306 dihedrals
33: Making cmap torsions...
33: There are 78 dihedrals, 82 impropers, 231 angles
33: 232 pairs, 156 bonds and 0 virtual sites
33: Total mass 1662.887 a.m.u.
33: Total charge -0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos53a6 force field in directory gromos53a6.ff
33:
33: going to rename gromos53a6.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
33: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 117
33:
33: Reading residue database... (Gromos53a6)
33: Processing chain 1 (117 atoms, 16 residues)
33: Identified residue LYS50 as a starting terminus.
33: Identified residue PRO65 as a ending terminus.
33: Start terminus LYS-50: NH3+
33: End terminus PRO-65: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 152 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
33: The Gromos53a6 force field and the spce water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/11 (322 ms)
33: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/12
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
33: Using default: not generating all possible dihedrals
33: Using default: excluding 3 bonded neighbors
33: Using default: generating 1,4 H--H interactions
33: Using default: removing proper dihedrals found on the same bond as a proper dihedral
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 25 donors and 23 acceptors were found.
33: There are 41 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33: Making bonds...
33: Number of bonds was 174, now 169
33: Marked 39 virtual sites
33: Added 4 dummy masses
33: Added 8 new constraints
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 267 pairs
33: Before cleaning: 312 dihedrals
33: Making cmap torsions...
33: There are 90 dihedrals, 79 impropers, 245 angles
33: 267 pairs, 169 bonds and 39 virtual sites
33: Total mass 1846.116 a.m.u.
33: Total charge -0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos53a6 force field in directory gromos53a6.ff
33:
33: going to rename gromos53a6.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 128
33:
33: Reading residue database... (Gromos53a6)
33: Processing chain 1 (128 atoms, 16 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 167 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
33: The Gromos53a6 force field and the spce water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/12 (342 ms)
33: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/13
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
33: Using default: not generating all possible dihedrals
33: Using default: excluding 3 bonded neighbors
33: Using default: generating 1,4 H--H interactions
33: Using default: removing proper dihedrals found on the same bond as a proper dihedral
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 30 donors and 22 acceptors were found.
33: There are 36 hydrogen bonds
33: Will use HISE for residue 29
33: Will use HISE for residue 32
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS27 HIS29
33: SG90 NE2111
33: HIS29 NE2111 0.987
33: HIS32 NE2135 1.590 1.155
33: Making bonds...
33: Number of bonds was 220, now 215
33: Marked 57 virtual sites
33: Added 4 dummy masses
33: Added 10 new constraints
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 273 pairs
33: Before cleaning: 443 dihedrals
33: Making cmap torsions...
33: There are 93 dihedrals, 138 impropers, 324 angles
33: 273 pairs, 215 bonds and 55 virtual sites
33: Total mass 2088.361 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos53a6 force field in directory gromos53a6.ff
33:
33: going to rename gromos53a6.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
33: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 149
33:
33: Reading residue database... (Gromos53a6)
33: Processing chain 1 (149 atoms, 16 residues)
33: Identified residue THR18 as a starting terminus.
33: Identified residue PHE33 as a ending terminus.
33: Start terminus THR-18: NH3+
33: End terminus PHE-33: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 206 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
33: The Gromos53a6 force field and the spce water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/13 (401 ms)
33: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/14
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
33: Using default: not generating all possible dihedrals
33: Using default: excluding 3 bonded neighbors
33: Using default: generating 1,4 H--H interactions
33: Using default: removing proper dihedrals found on the same bond as a proper dihedral
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 22 acceptors were found.
33: There are 26 hydrogen bonds
33: Will use HISE for residue 45
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS45
33: NE295
33: MET46 SD102 1.078
33: Making bonds...
33: Number of bonds was 181, now 176
33: Marked 38 virtual sites
33: Added 4 dummy masses
33: Added 8 new constraints
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 242 pairs
33: Before cleaning: 356 dihedrals
33: Making cmap torsions...
33: There are 81 dihedrals, 104 impropers, 264 angles
33: 242 pairs, 176 bonds and 38 virtual sites
33: Total mass 1861.132 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos53a6 force field in directory gromos53a6.ff
33:
33: going to rename gromos53a6.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
33: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 132
33:
33: Reading residue database... (Gromos53a6)
33: Processing chain 1 (132 atoms, 16 residues)
33: Identified residue ALA34 as a starting terminus.
33: Identified residue ALA49 as a ending terminus.
33: Start terminus ALA-34: NH3+
33: End terminus ALA-49: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 170 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
33: The Gromos53a6 force field and the spce water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/14 (360 ms)
33: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/15
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
33: Using default: not generating all possible dihedrals
33: Using default: excluding 3 bonded neighbors
33: Using default: generating 1,4 H--H interactions
33: Using default: removing proper dihedrals found on the same bond as a proper dihedral
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 21 acceptors were found.
33: There are 30 hydrogen bonds
33: Will use HISE for residue 60
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS60
33: NE285
33: CYS62 SG98 0.803
33: Making bonds...
33: Number of bonds was 161, now 156
33: Marked 35 virtual sites
33: Added 4 dummy masses
33: Added 10 new constraints
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 232 pairs
33: Before cleaning: 306 dihedrals
33: Making cmap torsions...
33: There are 78 dihedrals, 82 impropers, 231 angles
33: 232 pairs, 156 bonds and 33 virtual sites
33: Total mass 1662.887 a.m.u.
33: Total charge -0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos53a6 force field in directory gromos53a6.ff
33:
33: going to rename gromos53a6.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
33: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 117
33:
33: Reading residue database... (Gromos53a6)
33: Processing chain 1 (117 atoms, 16 residues)
33: Identified residue LYS50 as a starting terminus.
33: Identified residue PRO65 as a ending terminus.
33: Start terminus LYS-50: NH3+
33: End terminus PRO-65: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 152 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
33: The Gromos53a6 force field and the spce water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/15 (324 ms)
33: [----------] 16 tests from ForGromos53a6/Pdb2gmxTest (5761 ms total)
33:
33: [----------] Global test environment tear-down
33: [==========] 32 tests from 2 test cases ran. (11000 ms total)
33: [ PASSED ] 32 tests.
33/52 Test #33: Pdb2gmx2Test ........................ Passed 11.07 sec
test 34
Start 34: Pdb2gmx3Test
34: Test command: /<<PKGBUILDDIR>>/build/basic/bin/pdb2gmx3-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/Pdb2gmx3Test.xml"
34: Test timeout computed to be: 30
34: [==========] Running 28 tests from 4 test cases.
34: [----------] Global test environment set-up.
34: [----------] 8 tests from ForAmber99sb_ildn/Pdb2gmxTest
34: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/0
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 25 donors and 23 acceptors were found.
34: There are 41 hydrogen bonds
34: Will use HISE for residue 8
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: CYS3 HIS8
34: SG9 NE251
34: HIS8 NE251 1.055
34: MET12 SD83 0.763 0.990
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
34: Making bonds...
34: Number of bonds was 255, now 254
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 653 pairs
34: Before cleaning: 691 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 691 dihedrals, 51 impropers, 457 angles
34: 650 pairs, 254 bonds and 0 virtual sites
34: Total mass 1846.132 a.m.u.
34: Total charge 0.000 e
34: Writing topology
34:
34: Writing coordinate file...
34:
34: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
34:
34: going to rename amber99sb-ildn.ff/aminoacids.r2b
34: going to rename amber99sb-ildn.ff/dna.r2b
34: going to rename amber99sb-ildn.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
34: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records or chain id changing.
34: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
34:
34: chain #res #atoms
34: 1 ' ' 16 128
34:
34: Reading residue database... (Amber99sb-ildn)
34: Processing chain 1 (128 atoms, 16 residues)
34: Identified residue ALA2 as a starting terminus.
34: Identified residue SER17 as a ending terminus.
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 16 residues with 252 atoms
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
34: The Amber99sb-ildn force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/0 (491 ms)
34: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/1
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 30 donors and 22 acceptors were found.
34: There are 36 hydrogen bonds
34: Will use HISE for residue 29
34: Will use HISE for residue 32
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: CYS27 HIS29
34: SG90 NE2111
34: HIS29 NE2111 0.987
34: HIS32 NE2135 1.590 1.155
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
34: Making bonds...
34: Number of bonds was 291, now 290
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 748 pairs
34: Before cleaning: 788 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 788 dihedrals, 72 impropers, 516 angles
34: 736 pairs, 290 bonds and 0 virtual sites
34: Total mass 2088.366 a.m.u.
34: Total charge 1.000 e
34: Writing topology
34:
34: Writing coordinate file...
34:
34: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
34:
34: going to rename amber99sb-ildn.ff/aminoacids.r2b
34: going to rename amber99sb-ildn.ff/dna.r2b
34: going to rename amber99sb-ildn.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
34: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records or chain id changing.
34: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
34:
34: chain #res #atoms
34: 1 ' ' 16 149
34:
34: Reading residue database... (Amber99sb-ildn)
34: Processing chain 1 (149 atoms, 16 residues)
34: Identified residue THR18 as a starting terminus.
34: Identified residue PHE33 as a ending terminus.
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 16 residues with 281 atoms
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
34: The Amber99sb-ildn force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/1 (498 ms)
34: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/2
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 22 donors and 22 acceptors were found.
34: There are 26 hydrogen bonds
34: Will use HISE for residue 45
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: HIS45
34: NE295
34: MET46 SD102 1.078
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
34: Making bonds...
34: Number of bonds was 262, now 261
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 676 pairs
34: Before cleaning: 727 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 727 dihedrals, 56 impropers, 472 angles
34: 667 pairs, 261 bonds and 0 virtual sites
34: Total mass 1861.124 a.m.u.
34: Total charge -1.000 e
34: Writing topology
34:
34: Writing coordinate file...
34:
34: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
34:
34: going to rename amber99sb-ildn.ff/aminoacids.r2b
34: going to rename amber99sb-ildn.ff/dna.r2b
34: going to rename amber99sb-ildn.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
34: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records or chain id changing.
34: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
34:
34: chain #res #atoms
34: 1 ' ' 16 132
34:
34: Reading residue database... (Amber99sb-ildn)
34: Processing chain 1 (132 atoms, 16 residues)
34: Identified residue ALA34 as a starting terminus.
34: Identified residue ALA49 as a ending terminus.
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 16 residues with 255 atoms
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
34: The Amber99sb-ildn force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/2 (452 ms)
34: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/3
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 22 donors and 21 acceptors were found.
34: There are 30 hydrogen bonds
34: Will use HISE for residue 60
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: HIS60
34: NE285
34: CYS62 SG98 0.803
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
34: Making bonds...
34: Number of bonds was 233, now 232
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 603 pairs
34: Before cleaning: 634 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 634 dihedrals, 48 impropers, 419 angles
34: 597 pairs, 232 bonds and 0 virtual sites
34: Total mass 1662.888 a.m.u.
34: Total charge -0.000 e
34: Writing topology
34:
34: Writing coordinate file...
34:
34: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
34:
34: going to rename amber99sb-ildn.ff/aminoacids.r2b
34: going to rename amber99sb-ildn.ff/dna.r2b
34: going to rename amber99sb-ildn.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
34: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records or chain id changing.
34: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
34:
34: chain #res #atoms
34: 1 ' ' 16 117
34:
34: Reading residue database... (Amber99sb-ildn)
34: Processing chain 1 (117 atoms, 16 residues)
34: Identified residue LYS50 as a starting terminus.
34: Identified residue PRO65 as a ending terminus.
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 16 residues with 228 atoms
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
34: The Amber99sb-ildn force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/3 (406 ms)
34: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/4
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 25 donors and 23 acceptors were found.
34: There are 41 hydrogen bonds
34: Will use HISE for residue 8
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: CYS3 HIS8
34: SG9 NE251
34: HIS8 NE251 1.055
34: MET12 SD83 0.763 0.990
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
34: Making bonds...
34: Number of bonds was 255, now 254
34: Marked 124 virtual sites
34: Added 16 dummy masses
34: Added 26 new constraints
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 653 pairs
34: Before cleaning: 691 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 691 dihedrals, 51 impropers, 457 angles
34: 650 pairs, 254 bonds and 130 virtual sites
34: Total mass 1846.132 a.m.u.
34: Total charge 0.000 e
34: Writing topology
34:
34: Writing coordinate file...
34:
34: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
34:
34: going to rename amber99sb-ildn.ff/aminoacids.r2b
34: going to rename amber99sb-ildn.ff/dna.r2b
34: going to rename amber99sb-ildn.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
34: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records or chain id changing.
34: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
34:
34: chain #res #atoms
34: 1 ' ' 16 128
34:
34: Reading residue database... (Amber99sb-ildn)
34: Processing chain 1 (128 atoms, 16 residues)
34: Identified residue ALA2 as a starting terminus.
34: Identified residue SER17 as a ending terminus.
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 16 residues with 252 atoms
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
34: The Amber99sb-ildn force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/4 (478 ms)
34: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/5
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 30 donors and 22 acceptors were found.
34: There are 36 hydrogen bonds
34: Will use HISE for residue 29
34: Will use HISE for residue 32
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: CYS27 HIS29
34: SG90 NE2111
34: HIS29 NE2111 0.987
34: HIS32 NE2135 1.590 1.155
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
34: Making bonds...
34: Number of bonds was 291, now 290
34: Marked 132 virtual sites
34: Added 10 dummy masses
34: Added 19 new constraints
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 748 pairs
34: Before cleaning: 788 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 788 dihedrals, 72 impropers, 516 angles
34: 736 pairs, 290 bonds and 133 virtual sites
34: Total mass 2088.366 a.m.u.
34: Total charge 1.000 e
34: Writing topology
34:
34: Writing coordinate file...
34:
34: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
34:
34: going to rename amber99sb-ildn.ff/aminoacids.r2b
34: going to rename amber99sb-ildn.ff/dna.r2b
34: going to rename amber99sb-ildn.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
34: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records or chain id changing.
34: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
34:
34: chain #res #atoms
34: 1 ' ' 16 149
34:
34: Reading residue database... (Amber99sb-ildn)
34: Processing chain 1 (149 atoms, 16 residues)
34: Identified residue THR18 as a starting terminus.
34: Identified residue PHE33 as a ending terminus.
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 16 residues with 281 atoms
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
34: The Amber99sb-ildn force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/5 (523 ms)
34: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/6
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 22 donors and 22 acceptors were found.
34: There are 26 hydrogen bonds
34: Will use HISE for residue 45
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: HIS45
34: NE295
34: MET46 SD102 1.078
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
34: Making bonds...
34: Number of bonds was 262, now 261
34: Marked 123 virtual sites
34: Added 22 dummy masses
34: Added 35 new constraints
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 676 pairs
34: Before cleaning: 727 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 727 dihedrals, 56 impropers, 472 angles
34: 667 pairs, 261 bonds and 132 virtual sites
34: Total mass 1861.124 a.m.u.
34: Total charge -1.000 e
34: Writing topology
34:
34: Writing coordinate file...
34:
34: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
34:
34: going to rename amber99sb-ildn.ff/aminoacids.r2b
34: going to rename amber99sb-ildn.ff/dna.r2b
34: going to rename amber99sb-ildn.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
34: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records or chain id changing.
34: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
34:
34: chain #res #atoms
34: 1 ' ' 16 132
34:
34: Reading residue database... (Amber99sb-ildn)
34: Processing chain 1 (132 atoms, 16 residues)
34: Identified residue ALA34 as a starting terminus.
34: Identified residue ALA49 as a ending terminus.
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 16 residues with 255 atoms
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
34: The Amber99sb-ildn force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/6 (494 ms)
34: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/7
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 22 donors and 21 acceptors were found.
34: There are 30 hydrogen bonds
34: Will use HISE for residue 60
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: HIS60
34: NE285
34: CYS62 SG98 0.803
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
34: Making bonds...
34: Number of bonds was 233, now 232
34: Marked 111 virtual sites
34: Added 18 dummy masses
34: Added 31 new constraints
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 603 pairs
34: Before cleaning: 634 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 634 dihedrals, 48 impropers, 419 angles
34: 597 pairs, 232 bonds and 116 virtual sites
34: Total mass 1662.888 a.m.u.
34: Total charge -0.000 e
34: Writing topology
34:
34: Writing coordinate file...
34:
34: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
34:
34: going to rename amber99sb-ildn.ff/aminoacids.r2b
34: going to rename amber99sb-ildn.ff/dna.r2b
34: going to rename amber99sb-ildn.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
34: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records or chain id changing.
34: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
34:
34: chain #res #atoms
34: 1 ' ' 16 117
34:
34: Reading residue database... (Amber99sb-ildn)
34: Processing chain 1 (117 atoms, 16 residues)
34: Identified residue LYS50 as a starting terminus.
34: Identified residue PRO65 as a ending terminus.
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 16 residues with 228 atoms
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
34: The Amber99sb-ildn force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/7 (435 ms)
34: [----------] 8 tests from ForAmber99sb_ildn/Pdb2gmxTest (3781 ms total)
34:
34: [----------] 8 tests from ForCharmm27/Pdb2gmxTest
34: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/0
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 25 donors and 23 acceptors were found.
34: There are 41 hydrogen bonds
34: Will use HISE for residue 8
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: CYS3 HIS8
34: SG9 NE251
34: HIS8 NE251 1.055
34: MET12 SD83 0.763 0.990
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 254, now 254
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 653 pairs
34: Before cleaning: 663 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 14 cmap torsion pairs
34: There are 663 dihedrals, 48 impropers, 457 angles
34: 650 pairs, 254 bonds and 0 virtual sites
34: Total mass 1846.115 a.m.u.
34: Total charge 0.000 e
34: Writing topology
34:
34: Writing coordinate file...
34:
34: Using the Charmm27 force field in directory charmm27.ff
34:
34: going to rename charmm27.ff/aminoacids.r2b
34: going to rename charmm27.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
34: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records or chain id changing.
34: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
34:
34: chain #res #atoms
34: 1 ' ' 16 128
34:
34: Reading residue database... (Charmm27)
34: Processing chain 1 (128 atoms, 16 residues)
34: Identified residue ALA2 as a starting terminus.
34: Identified residue SER17 as a ending terminus.
34: Start terminus ALA-2: NH3+
34: End terminus SER-17: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 16 residues with 252 atoms
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
34: The Charmm27 force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/0 (472 ms)
34: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/1
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 30 donors and 22 acceptors were found.
34: There are 36 hydrogen bonds
34: Will use HISE for residue 29
34: Will use HISE for residue 32
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: CYS27 HIS29
34: SG90 NE2111
34: HIS29 NE2111 0.987
34: HIS32 NE2135 1.590 1.155
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 290, now 290
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 748 pairs
34: Before cleaning: 778 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 14 cmap torsion pairs
34: There are 778 dihedrals, 49 impropers, 516 angles
34: 736 pairs, 290 bonds and 0 virtual sites
34: Total mass 2088.361 a.m.u.
34: Total charge 1.000 e
34: Writing topology
34:
34: Writing coordinate file...
34:
34: Using the Charmm27 force field in directory charmm27.ff
34:
34: going to rename charmm27.ff/aminoacids.r2b
34: going to rename charmm27.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
34: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records or chain id changing.
34: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
34:
34: chain #res #atoms
34: 1 ' ' 16 149
34:
34: Reading residue database... (Charmm27)
34: Processing chain 1 (149 atoms, 16 residues)
34: Identified residue THR18 as a starting terminus.
34: Identified residue PHE33 as a ending terminus.
34: Start terminus THR-18: NH3+
34: End terminus PHE-33: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 16 residues with 281 atoms
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
34: The Charmm27 force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/1 (493 ms)
34: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/2
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 22 donors and 22 acceptors were found.
34: There are 26 hydrogen bonds
34: Will use HISE for residue 45
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: HIS45
34: NE295
34: MET46 SD102 1.078
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 261, now 261
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 676 pairs
34: Before cleaning: 696 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 14 cmap torsion pairs
34: There are 696 dihedrals, 39 impropers, 472 angles
34: 667 pairs, 261 bonds and 0 virtual sites
34: Total mass 1861.130 a.m.u.
34: Total charge -1.000 e
34: Writing topology
34:
34: Writing coordinate file...
34:
34: Using the Charmm27 force field in directory charmm27.ff
34:
34: going to rename charmm27.ff/aminoacids.r2b
34: going to rename charmm27.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
34: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records or chain id changing.
34: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
34:
34: chain #res #atoms
34: 1 ' ' 16 132
34:
34: Reading residue database... (Charmm27)
34: Processing chain 1 (132 atoms, 16 residues)
34: Identified residue ALA34 as a starting terminus.
34: Identified residue ALA49 as a ending terminus.
34: Start terminus ALA-34: NH3+
34: End terminus ALA-49: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 16 residues with 255 atoms
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
34: The Charmm27 force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/2 (430 ms)
34: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/3
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 22 donors and 21 acceptors were found.
34: There are 30 hydrogen bonds
34: Will use HISE for residue 60
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: HIS60
34: NE285
34: CYS62 SG98 0.803
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 232, now 232
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 603 pairs
34: Before cleaning: 618 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 14 cmap torsion pairs
34: There are 618 dihedrals, 38 impropers, 419 angles
34: 597 pairs, 232 bonds and 0 virtual sites
34: Total mass 1662.885 a.m.u.
34: Total charge 0.000 e
34: Writing topology
34:
34: Writing coordinate file...
34:
34: Using the Charmm27 force field in directory charmm27.ff
34:
34: going to rename charmm27.ff/aminoacids.r2b
34: going to rename charmm27.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
34: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records or chain id changing.
34: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
34:
34: chain #res #atoms
34: 1 ' ' 16 117
34:
34: Reading residue database... (Charmm27)
34: Processing chain 1 (117 atoms, 16 residues)
34: Identified residue LYS50 as a starting terminus.
34: Identified residue PRO65 as a ending terminus.
34: Start terminus LYS-50: NH3+
34: End terminus PRO-65: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 16 residues with 228 atoms
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
34: The Charmm27 force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/3 (377 ms)
34: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/4
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 25 donors and 23 acceptors were found.
34: There are 41 hydrogen bonds
34: Will use HISE for residue 8
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: CYS3 HIS8
34: SG9 NE251
34: HIS8 NE251 1.055
34: MET12 SD83 0.763 0.990
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 254, now 254
34: Marked 124 virtual sites
34: Added 16 dummy masses
34: Added 26 new constraints
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 653 pairs
34: Before cleaning: 663 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 14 cmap torsion pairs
34: There are 663 dihedrals, 48 impropers, 457 angles
34: 650 pairs, 254 bonds and 130 virtual sites
34: Total mass 1846.115 a.m.u.
34: Total charge 0.000 e
34: Writing topology
34:
34: Writing coordinate file...
34:
34: Using the Charmm27 force field in directory charmm27.ff
34:
34: going to rename charmm27.ff/aminoacids.r2b
34: going to rename charmm27.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
34: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records or chain id changing.
34: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
34:
34: chain #res #atoms
34: 1 ' ' 16 128
34:
34: Reading residue database... (Charmm27)
34: Processing chain 1 (128 atoms, 16 residues)
34: Identified residue ALA2 as a starting terminus.
34: Identified residue SER17 as a ending terminus.
34: Start terminus ALA-2: NH3+
34: End terminus SER-17: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 16 residues with 252 atoms
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
34: The Charmm27 force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/4 (470 ms)
34: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/5
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 30 donors and 22 acceptors were found.
34: There are 36 hydrogen bonds
34: Will use HISE for residue 29
34: Will use HISE for residue 32
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: CYS27 HIS29
34: SG90 NE2111
34: HIS29 NE2111 0.987
34: HIS32 NE2135 1.590 1.155
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 290, now 290
34: Marked 132 virtual sites
34: Added 10 dummy masses
34: Added 19 new constraints
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 748 pairs
34: Before cleaning: 778 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 14 cmap torsion pairs
34: There are 778 dihedrals, 49 impropers, 516 angles
34: 736 pairs, 290 bonds and 133 virtual sites
34: Total mass 2088.361 a.m.u.
34: Total charge 1.000 e
34: Writing topology
34:
34: Writing coordinate file...
34:
34: Using the Charmm27 force field in directory charmm27.ff
34:
34: going to rename charmm27.ff/aminoacids.r2b
34: going to rename charmm27.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
34: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records or chain id changing.
34: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
34:
34: chain #res #atoms
34: 1 ' ' 16 149
34:
34: Reading residue database... (Charmm27)
34: Processing chain 1 (149 atoms, 16 residues)
34: Identified residue THR18 as a starting terminus.
34: Identified residue PHE33 as a ending terminus.
34: Start terminus THR-18: NH3+
34: End terminus PHE-33: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 16 residues with 281 atoms
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
34: The Charmm27 force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/5 (512 ms)
34: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/6
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 22 donors and 22 acceptors were found.
34: There are 26 hydrogen bonds
34: Will use HISE for residue 45
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: HIS45
34: NE295
34: MET46 SD102 1.078
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 261, now 261
34: Marked 123 virtual sites
34: Added 22 dummy masses
34: Added 35 new constraints
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 676 pairs
34: Before cleaning: 696 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 14 cmap torsion pairs
34: There are 696 dihedrals, 39 impropers, 472 angles
34: 667 pairs, 261 bonds and 132 virtual sites
34: Total mass 1861.130 a.m.u.
34: Total charge -1.000 e
34: Writing topology
34:
34: Writing coordinate file...
34:
34: Using the Charmm27 force field in directory charmm27.ff
34:
34: going to rename charmm27.ff/aminoacids.r2b
34: going to rename charmm27.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
34: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records or chain id changing.
34: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
34:
34: chain #res #atoms
34: 1 ' ' 16 132
34:
34: Reading residue database... (Charmm27)
34: Processing chain 1 (132 atoms, 16 residues)
34: Identified residue ALA34 as a starting terminus.
34: Identified residue ALA49 as a ending terminus.
34: Start terminus ALA-34: NH3+
34: End terminus ALA-49: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 16 residues with 255 atoms
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
34: The Charmm27 force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/6 (486 ms)
34: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/7
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 22 donors and 21 acceptors were found.
34: There are 30 hydrogen bonds
34: Will use HISE for residue 60
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: HIS60
34: NE285
34: CYS62 SG98 0.803
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 232, now 232
34: Marked 111 virtual sites
34: Added 18 dummy masses
34: Added 31 new constraints
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 603 pairs
34: Before cleaning: 618 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 14 cmap torsion pairs
34: There are 618 dihedrals, 38 impropers, 419 angles
34: 597 pairs, 232 bonds and 116 virtual sites
34: Total mass 1662.885 a.m.u.
34: Total charge 0.000 e
34: Writing topology
34:
34: Writing coordinate file...
34:
34: Using the Charmm27 force field in directory charmm27.ff
34:
34: going to rename charmm27.ff/aminoacids.r2b
34: going to rename charmm27.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
34: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records or chain id changing.
34: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
34:
34: chain #res #atoms
34: 1 ' ' 16 117
34:
34: Reading residue database... (Charmm27)
34: Processing chain 1 (117 atoms, 16 residues)
34: Identified residue LYS50 as a starting terminus.
34: Identified residue PRO65 as a ending terminus.
34: Start terminus LYS-50: NH3+
34: End terminus PRO-65: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 16 residues with 228 atoms
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
34: The Charmm27 force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/7 (426 ms)
34: [----------] 8 tests from ForCharmm27/Pdb2gmxTest (3670 ms total)
34:
34: [----------] 8 tests from ChainSep/Pdb2gmxTest
34: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/0
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 25 donors and 23 acceptors were found.
34: There are 41 hydrogen bonds
34: Will use HISE for residue 8
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: CYS3 HIS8
34: SG9 NE251
34: HIS8 NE251 1.055
34: MET12 SD83 0.763 0.990
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 258, now 258
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 651 pairs
34: Before cleaning: 661 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 10 cmap torsion pairs
34: There are 661 dihedrals, 46 impropers, 463 angles
34: 648 pairs, 258 bonds and 0 virtual sites
34: Total mass 1882.146 a.m.u.
34: Total charge 0.000 e
34: Writing topology
34:
34: Writing coordinate file...
34:
34: Using the Charmm27 force field in directory charmm27.ff
34:
34: going to rename charmm27.ff/aminoacids.r2b
34: going to rename charmm27.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
34: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on changing chain id only (ignoring TER records).
34:
34: Merged chains into joint molecule definitions at 2 places.
34:
34: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms
34:
34: chain #res #atoms
34: 1 'A' 16 127
34:
34: Reading residue database... (Charmm27)
34: Processing chain 1 'A' (127 atoms, 16 residues)
34: Identified residue ALA2 as a starting terminus.
34: Identified residue GLU5 as a ending terminus.
34: Identified residue PHE6 as a starting terminus.
34: Identified residue MET12 as a ending terminus.
34: Identified residue ASN13 as a starting terminus.
34: Identified residue SER17 as a ending terminus.
34: Start terminus ALA-2: NH3+
34: End terminus GLU-5: COO-
34: Start terminus PHE-6: NH3+
34: End terminus MET-12: COO-
34: Start terminus ASN-13: NH3+
34: End terminus SER-17: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 16 residues with 258 atoms
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
34: The Charmm27 force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/0 (441 ms)
34: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/1
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
34: 8 out of 8 lines of specbond.dat converted successfully
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 50, now 50
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 123 pairs
34: Before cleaning: 123 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 2 cmap torsion pairs
34: There are 123 dihedrals, 9 impropers, 88 angles
34: 123 pairs, 50 bonds and 0 virtual sites
34: Total mass 434.421 a.m.u.
34: Total charge -2.000 e
34: Writing topology
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 10 donors and 7 acceptors were found.
34: There are 7 hydrogen bonds
34: Will use HISE for residue 8
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: HIS8
34: NE223
34: MET12 SD55 0.990
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 125, now 125
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 317 pairs
34: Before cleaning: 322 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 5 cmap torsion pairs
34: There are 322 dihedrals, 19 impropers, 227 angles
34: 314 pairs, 125 bonds and 0 virtual sites
34: Total mass 846.083 a.m.u.
34: Total charge 1.000 e
34: Writing topology
34: 8 out of 8 lines of specbond.dat converted successfully
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 83, now 83
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 211 pairs
34: Before cleaning: 216 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 3 cmap torsion pairs
34: There are 216 dihedrals, 18 impropers, 148 angles
34: 211 pairs, 83 bonds and 0 virtual sites
34: Total mass 601.643 a.m.u.
34: Total charge 1.000 e
34: Writing topology
34: Now there are 258 atoms and 16 residues
34: Total mass in system 1882.146 a.m.u.
34: Total charge in system 0.000 e
34:
34: Writing coordinate file...
34:
34: Using the Charmm27 force field in directory charmm27.ff
34:
34: going to rename charmm27.ff/aminoacids.r2b
34: going to rename charmm27.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
34: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on changing chain id only (ignoring TER records).
34: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms
34:
34: chain #res #atoms
34: 1 'A' 4 28
34: 2 'B' 7 58
34: 3 'C' 5 41
34:
34: Reading residue database... (Charmm27)
34: Processing chain 1 'A' (28 atoms, 4 residues)
34: Identified residue ALA2 as a starting terminus.
34: Identified residue GLU5 as a ending terminus.
34: Start terminus ALA-2: NH3+
34: End terminus GLU-5: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 4 residues with 51 atoms
34: Chain time...
34: Processing chain 2 'B' (58 atoms, 7 residues)
34: Identified residue PHE6 as a starting terminus.
34: Identified residue MET12 as a ending terminus.
34: Start terminus PHE-6: NH3+
34: End terminus MET-12: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 7 residues with 124 atoms
34: Chain time...
34: Processing chain 3 'C' (41 atoms, 5 residues)
34: Identified residue ASN13 as a starting terminus.
34: Identified residue SER17 as a ending terminus.
34: Start terminus ASN-13: NH3+
34: End terminus SER-17: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 5 residues with 83 atoms
34: Chain time...
34: Including chain 1 in system: 51 atoms 4 residues
34: Including chain 2 in system: 124 atoms 7 residues
34: Including chain 3 in system: 83 atoms 5 residues
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
34: The Charmm27 force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/1 (291 ms)
34: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/2
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 25 donors and 23 acceptors were found.
34: There are 41 hydrogen bonds
34: Will use HISE for residue 8
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: CYS3 HIS8
34: SG9 NE251
34: HIS8 NE251 1.055
34: MET12 SD83 0.763 0.990
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 258, now 258
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 651 pairs
34: Before cleaning: 661 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 10 cmap torsion pairs
34: There are 661 dihedrals, 46 impropers, 463 angles
34: 648 pairs, 258 bonds and 0 virtual sites
34: Total mass 1882.146 a.m.u.
34: Total charge 0.000 e
34: Writing topology
34:
34: Writing coordinate file...
34:
34: Using the Charmm27 force field in directory charmm27.ff
34:
34: going to rename charmm27.ff/aminoacids.r2b
34: going to rename charmm27.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
34: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records only (ignoring chain id).
34:
34: Merged chains into joint molecule definitions at 2 places.
34:
34: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms
34:
34: chain #res #atoms
34: 1 'A' 16 127
34:
34: Reading residue database... (Charmm27)
34: Processing chain 1 'A' (127 atoms, 16 residues)
34: Identified residue ALA2 as a starting terminus.
34: Identified residue ILE9 as a ending terminus.
34: Identified residue LYS10 as a starting terminus.
34: Identified residue MET12 as a ending terminus.
34: Identified residue ASN13 as a starting terminus.
34: Identified residue SER17 as a ending terminus.
34: Start terminus ALA-2: NH3+
34: End terminus ILE-9: COO-
34: Start terminus LYS-10: NH3+
34: End terminus MET-12: COO-
34: Start terminus ASN-13: NH3+
34: End terminus SER-17: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 16 residues with 258 atoms
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
34: The Charmm27 force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/2 (441 ms)
34: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/3
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 10 donors and 12 acceptors were found.
34: There are 13 hydrogen bonds
34: Will use HISE for residue 8
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: CYS3
34: SG9
34: HIS8 NE251 1.055
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 115, now 115
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 288 pairs
34: Before cleaning: 293 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 6 cmap torsion pairs
34: There are 293 dihedrals, 23 impropers, 203 angles
34: 285 pairs, 115 bonds and 0 virtual sites
34: Total mass 888.952 a.m.u.
34: Total charge -2.000 e
34: Writing topology
34: 8 out of 8 lines of specbond.dat converted successfully
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 60, now 60
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 152 pairs
34: Before cleaning: 152 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 1 cmap torsion pairs
34: There are 152 dihedrals, 5 impropers, 112 angles
34: 152 pairs, 60 bonds and 0 virtual sites
34: Total mass 391.552 a.m.u.
34: Total charge 1.000 e
34: Writing topology
34: 8 out of 8 lines of specbond.dat converted successfully
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 83, now 83
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 211 pairs
34: Before cleaning: 216 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 3 cmap torsion pairs
34: There are 216 dihedrals, 18 impropers, 148 angles
34: 211 pairs, 83 bonds and 0 virtual sites
34: Total mass 601.643 a.m.u.
34: Total charge 1.000 e
34: Writing topology
34: Now there are 258 atoms and 16 residues
34: Total mass in system 1882.146 a.m.u.
34: Total charge in system 0.000 e
34:
34: Writing coordinate file...
34:
34: Using the Charmm27 force field in directory charmm27.ff
34:
34: going to rename charmm27.ff/aminoacids.r2b
34: going to rename charmm27.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
34: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records only (ignoring chain id).
34: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms
34:
34: chain #res #atoms
34: 1 'A' 8 61
34: 2 'B' 3 25
34: 3 'C' 5 41
34:
34: Reading residue database... (Charmm27)
34: Processing chain 1 'A' (61 atoms, 8 residues)
34: Identified residue ALA2 as a starting terminus.
34: Identified residue ILE9 as a ending terminus.
34: Start terminus ALA-2: NH3+
34: End terminus ILE-9: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 8 residues with 114 atoms
34: Chain time...
34: Processing chain 2 'B' (25 atoms, 3 residues)
34: Identified residue LYS10 as a starting terminus.
34: Identified residue MET12 as a ending terminus.
34: Start terminus LYS-10: NH3+
34: End terminus MET-12: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 3 residues with 61 atoms
34: Chain time...
34: Processing chain 3 'C' (41 atoms, 5 residues)
34: Identified residue ASN13 as a starting terminus.
34: Identified residue SER17 as a ending terminus.
34: Start terminus ASN-13: NH3+
34: End terminus SER-17: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 5 residues with 83 atoms
34: Chain time...
34: Including chain 1 in system: 114 atoms 8 residues
34: Including chain 2 in system: 61 atoms 3 residues
34: Including chain 3 in system: 83 atoms 5 residues
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
34: The Charmm27 force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/3 (288 ms)
34: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/4
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 25 donors and 23 acceptors were found.
34: There are 41 hydrogen bonds
34: Will use HISE for residue 8
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: CYS3 HIS8
34: SG9 NE251
34: HIS8 NE251 1.055
34: MET12 SD83 0.763 0.990
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 260, now 260
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 650 pairs
34: Before cleaning: 660 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 8 cmap torsion pairs
34: There are 660 dihedrals, 45 impropers, 466 angles
34: 647 pairs, 260 bonds and 0 virtual sites
34: Total mass 1900.162 a.m.u.
34: Total charge 0.000 e
34: Writing topology
34:
34: Writing coordinate file...
34:
34: Using the Charmm27 force field in directory charmm27.ff
34:
34: going to rename charmm27.ff/aminoacids.r2b
34: going to rename charmm27.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
34: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records or chain id changing.
34:
34: Merged chains into joint molecule definitions at 3 places.
34:
34: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms
34:
34: chain #res #atoms
34: 1 'A' 16 127
34:
34: Reading residue database... (Charmm27)
34: Processing chain 1 'A' (127 atoms, 16 residues)
34: Identified residue ALA2 as a starting terminus.
34: Identified residue GLU5 as a ending terminus.
34: Identified residue PHE6 as a starting terminus.
34: Identified residue ILE9 as a ending terminus.
34: Identified residue LYS10 as a starting terminus.
34: Identified residue MET12 as a ending terminus.
34: Identified residue ASN13 as a starting terminus.
34: Identified residue SER17 as a ending terminus.
34: Start terminus ALA-2: NH3+
34: End terminus GLU-5: COO-
34: Start terminus PHE-6: NH3+
34: End terminus ILE-9: COO-
34: Start terminus LYS-10: NH3+
34: End terminus MET-12: COO-
34: Start terminus ASN-13: NH3+
34: End terminus SER-17: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 16 residues with 261 atoms
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
34: The Charmm27 force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/4 (442 ms)
34: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/5
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
34: 8 out of 8 lines of specbond.dat converted successfully
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 50, now 50
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 123 pairs
34: Before cleaning: 123 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 2 cmap torsion pairs
34: There are 123 dihedrals, 9 impropers, 88 angles
34: 123 pairs, 50 bonds and 0 virtual sites
34: Total mass 434.421 a.m.u.
34: Total charge -2.000 e
34: Writing topology
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 6 donors and 4 acceptors were found.
34: There are 3 hydrogen bonds
34: Will use HISE for residue 8
34: 8 out of 8 lines of specbond.dat converted successfully
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 67, now 67
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 164 pairs
34: Before cleaning: 169 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 2 cmap torsion pairs
34: There are 169 dihedrals, 13 impropers, 118 angles
34: 161 pairs, 67 bonds and 0 virtual sites
34: Total mass 472.547 a.m.u.
34: Total charge 0.000 e
34: Writing topology
34: 8 out of 8 lines of specbond.dat converted successfully
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 60, now 60
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 152 pairs
34: Before cleaning: 152 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 1 cmap torsion pairs
34: There are 152 dihedrals, 5 impropers, 112 angles
34: 152 pairs, 60 bonds and 0 virtual sites
34: Total mass 391.552 a.m.u.
34: Total charge 1.000 e
34: Writing topology
34: 8 out of 8 lines of specbond.dat converted successfully
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 83, now 83
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 211 pairs
34: Before cleaning: 216 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 3 cmap torsion pairs
34: There are 216 dihedrals, 18 impropers, 148 angles
34: 211 pairs, 83 bonds and 0 virtual sites
34: Total mass 601.643 a.m.u.
34: Total charge 1.000 e
34: Writing topology
34: Now there are 261 atoms and 16 residues
34: Total mass in system 1900.162 a.m.u.
34: Total charge in system 0.000 e
34:
34: Writing coordinate file...
34:
34: Using the Charmm27 force field in directory charmm27.ff
34:
34: going to rename charmm27.ff/aminoacids.r2b
34: going to rename charmm27.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
34: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records or chain id changing.
34: WARNING: Chain identifier 'B' is used in two non-sequential blocks.
34: They will be treated as separate chains unless you reorder your file.
34: There are 4 chains and 0 blocks of water and 16 residues with 127 atoms
34:
34: chain #res #atoms
34: 1 'A' 4 28
34: 2 'B' 4 33
34: 3 'B' 3 25
34: 4 'C' 5 41
34:
34: Reading residue database... (Charmm27)
34: Processing chain 1 'A' (28 atoms, 4 residues)
34: Identified residue ALA2 as a starting terminus.
34: Identified residue GLU5 as a ending terminus.
34: Start terminus ALA-2: NH3+
34: End terminus GLU-5: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 4 residues with 51 atoms
34: Chain time...
34: Processing chain 2 'B' (33 atoms, 4 residues)
34: Identified residue PHE6 as a starting terminus.
34: Identified residue ILE9 as a ending terminus.
34: Start terminus PHE-6: NH3+
34: End terminus ILE-9: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 4 residues with 66 atoms
34: Chain time...
34: Processing chain 3 'B' (25 atoms, 3 residues)
34: Identified residue LYS10 as a starting terminus.
34: Identified residue MET12 as a ending terminus.
34: Start terminus LYS-10: NH3+
34: End terminus MET-12: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 3 residues with 61 atoms
34: Chain time...
34: Processing chain 4 'C' (41 atoms, 5 residues)
34: Identified residue ASN13 as a starting terminus.
34: Identified residue SER17 as a ending terminus.
34: Start terminus ASN-13: NH3+
34: End terminus SER-17: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 5 residues with 83 atoms
34: Chain time...
34: Including chain 1 in system: 51 atoms 4 residues
34: Including chain 2 in system: 66 atoms 4 residues
34: Including chain 3 in system: 61 atoms 3 residues
34: Including chain 4 in system: 83 atoms 5 residues
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
34: The Charmm27 force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/5 (288 ms)
34: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/6
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 25 donors and 23 acceptors were found.
34: There are 41 hydrogen bonds
34: Will use HISE for residue 8
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: CYS3 HIS8
34: SG9 NE251
34: HIS8 NE251 1.055
34: MET12 SD83 0.763 0.990
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 256, now 256
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 652 pairs
34: Before cleaning: 662 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 12 cmap torsion pairs
34: There are 662 dihedrals, 47 impropers, 460 angles
34: 649 pairs, 256 bonds and 0 virtual sites
34: Total mass 1864.131 a.m.u.
34: Total charge 0.000 e
34: Writing topology
34:
34: Writing coordinate file...
34:
34: Using the Charmm27 force field in directory charmm27.ff
34:
34: going to rename charmm27.ff/aminoacids.r2b
34: going to rename charmm27.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
34: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records and chain id changing.
34:
34: Merged chains into joint molecule definitions at 1 places.
34:
34: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms
34:
34: chain #res #atoms
34: 1 'A' 16 127
34:
34: Reading residue database... (Charmm27)
34: Processing chain 1 'A' (127 atoms, 16 residues)
34: Identified residue ALA2 as a starting terminus.
34: Identified residue MET12 as a ending terminus.
34: Identified residue ASN13 as a starting terminus.
34: Identified residue SER17 as a ending terminus.
34: Start terminus ALA-2: NH3+
34: End terminus MET-12: COO-
34: Start terminus ASN-13: NH3+
34: End terminus SER-17: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 16 residues with 255 atoms
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
34: The Charmm27 force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/6 (419 ms)
34: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/7
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 14 donors and 15 acceptors were found.
34: There are 20 hydrogen bonds
34: Will use HISE for residue 8
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: CYS3 HIS8
34: SG9 NE251
34: HIS8 NE251 1.055
34: MET12 SD83 0.763 0.990
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 173, now 173
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 441 pairs
34: Before cleaning: 446 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 9 cmap torsion pairs
34: There are 446 dihedrals, 29 impropers, 312 angles
34: 438 pairs, 173 bonds and 0 virtual sites
34: Total mass 1262.488 a.m.u.
34: Total charge -1.000 e
34: Writing topology
34: 8 out of 8 lines of specbond.dat converted successfully
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 83, now 83
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 211 pairs
34: Before cleaning: 216 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 3 cmap torsion pairs
34: There are 216 dihedrals, 18 impropers, 148 angles
34: 211 pairs, 83 bonds and 0 virtual sites
34: Total mass 601.643 a.m.u.
34: Total charge 1.000 e
34: Writing topology
34: Now there are 255 atoms and 16 residues
34: Total mass in system 1864.131 a.m.u.
34: Total charge in system 0.000 e
34:
34: Writing coordinate file...
34:
34: Using the Charmm27 force field in directory charmm27.ff
34:
34: going to rename charmm27.ff/aminoacids.r2b
34: going to rename charmm27.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
34: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records and chain id changing.
34: There are 2 chains and 0 blocks of water and 16 residues with 127 atoms
34:
34: chain #res #atoms
34: 1 'A' 11 86
34: 2 'C' 5 41
34:
34: Reading residue database... (Charmm27)
34: Processing chain 1 'A' (86 atoms, 11 residues)
34: Identified residue ALA2 as a starting terminus.
34: Identified residue MET12 as a ending terminus.
34: Start terminus ALA-2: NH3+
34: End terminus MET-12: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 11 residues with 172 atoms
34: Chain time...
34: Processing chain 2 'C' (41 atoms, 5 residues)
34: Identified residue ASN13 as a starting terminus.
34: Identified residue SER17 as a ending terminus.
34: Start terminus ASN-13: NH3+
34: End terminus SER-17: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 5 residues with 83 atoms
34: Chain time...
34: Including chain 1 in system: 172 atoms 11 residues
34: Including chain 2 in system: 83 atoms 5 residues
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
34: The Charmm27 force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/7 (307 ms)
34: [----------] 8 tests from ChainSep/Pdb2gmxTest (2917 ms total)
34:
34: [----------] 4 tests from ChainChanges/Pdb2gmxTest
34: [ RUN ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/0
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
34: 8 out of 8 lines of specbond.dat converted successfully
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 35, now 35
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 83 pairs
34: Before cleaning: 83 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 1 cmap torsion pairs
34: There are 83 dihedrals, 6 impropers, 61 angles
34: 83 pairs, 35 bonds and 0 virtual sites
34: Total mass 306.314 a.m.u.
34: Total charge -1.000 e
34: Writing topology
34: 8 out of 8 lines of specbond.dat converted successfully
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 58, now 58
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 145 pairs
34: Before cleaning: 150 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 1 cmap torsion pairs
34: There are 150 dihedrals, 5 impropers, 103 angles
34: 142 pairs, 58 bonds and 0 virtual sites
34: Total mass 404.468 a.m.u.
34: Total charge -0.000 e
34: Writing topology
34: Now there are 93 atoms and 6 residues
34: Total mass in system 710.782 a.m.u.
34: Total charge in system -1.000 e
34:
34: Writing coordinate file...
34:
34: Using the Charmm27 force field in directory charmm27.ff
34:
34: going to rename charmm27.ff/aminoacids.r2b
34: going to rename charmm27.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb...
34: Read 'Fragments of peptides and ions', 47 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on changing chain id only (ignoring TER records).
34: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms
34:
34: chain #res #atoms
34: 1 'A' 3 19
34: 2 'B' 3 28
34:
34: Reading residue database... (Charmm27)
34: Processing chain 1 'A' (19 atoms, 3 residues)
34: Identified residue ALA2 as a starting terminus.
34: Identified residue ASP4 as a ending terminus.
34: Start terminus ALA-2: NH3+
34: End terminus ASP-4: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 3 residues with 36 atoms
34: Chain time...
34: Processing chain 2 'B' (28 atoms, 3 residues)
34: Identified residue THR18 as a starting terminus.
34: Identified residue TRP20 as a ending terminus.
34: Start terminus THR-18: NH3+
34: End terminus TRP-20: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 3 residues with 57 atoms
34: Chain time...
34: Including chain 1 in system: 36 atoms 3 residues
34: Including chain 2 in system: 57 atoms 3 residues
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb.
34: The Charmm27 force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/0 (209 ms)
34: [ RUN ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/1
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
34: 8 out of 8 lines of specbond.dat converted successfully
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 35, now 35
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 83 pairs
34: Before cleaning: 83 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 1 cmap torsion pairs
34: There are 83 dihedrals, 6 impropers, 61 angles
34: 83 pairs, 35 bonds and 0 virtual sites
34: Total mass 306.314 a.m.u.
34: Total charge -1.000 e
34: Writing topology
34: 8 out of 8 lines of specbond.dat converted successfully
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 58, now 58
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 145 pairs
34: Before cleaning: 150 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 1 cmap torsion pairs
34: There are 150 dihedrals, 5 impropers, 103 angles
34: 142 pairs, 58 bonds and 0 virtual sites
34: Total mass 404.468 a.m.u.
34: Total charge -0.000 e
34: Writing topology
34: Now there are 93 atoms and 6 residues
34: Total mass in system 710.782 a.m.u.
34: Total charge in system -1.000 e
34:
34: Writing coordinate file...
34:
34: Using the Charmm27 force field in directory charmm27.ff
34:
34: going to rename charmm27.ff/aminoacids.r2b
34: going to rename charmm27.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb...
34: Read 'Fragments of peptides and ions', 47 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records only (ignoring chain id).
34: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms
34:
34: chain #res #atoms
34: 1 'A' 3 19
34: 2 'B' 3 28
34:
34: Reading residue database... (Charmm27)
34: Processing chain 1 'A' (19 atoms, 3 residues)
34: Identified residue ALA2 as a starting terminus.
34: Identified residue ASP4 as a ending terminus.
34: Start terminus ALA-2: NH3+
34: End terminus ASP-4: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 3 residues with 36 atoms
34: Chain time...
34: Processing chain 2 'B' (28 atoms, 3 residues)
34: Identified residue THR18 as a starting terminus.
34: Identified residue TRP20 as a ending terminus.
34: Start terminus THR-18: NH3+
34: End terminus TRP-20: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 3 residues with 57 atoms
34: Chain time...
34: Including chain 1 in system: 36 atoms 3 residues
34: Including chain 2 in system: 57 atoms 3 residues
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb.
34: The Charmm27 force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/1 (207 ms)
34: [ RUN ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/2
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
34: 8 out of 8 lines of specbond.dat converted successfully
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 35, now 35
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 83 pairs
34: Before cleaning: 83 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 1 cmap torsion pairs
34: There are 83 dihedrals, 6 impropers, 61 angles
34: 83 pairs, 35 bonds and 0 virtual sites
34: Total mass 306.314 a.m.u.
34: Total charge -1.000 e
34: Writing topology
34: 8 out of 8 lines of specbond.dat converted successfully
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 58, now 58
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 145 pairs
34: Before cleaning: 150 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 1 cmap torsion pairs
34: There are 150 dihedrals, 5 impropers, 103 angles
34: 142 pairs, 58 bonds and 0 virtual sites
34: Total mass 404.468 a.m.u.
34: Total charge -0.000 e
34: Writing topology
34: Now there are 93 atoms and 6 residues
34: Total mass in system 710.782 a.m.u.
34: Total charge in system -1.000 e
34:
34: Writing coordinate file...
34:
34: Using the Charmm27 force field in directory charmm27.ff
34:
34: going to rename charmm27.ff/aminoacids.r2b
34: going to rename charmm27.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb...
34: Read 'Fragments of peptides and ions', 47 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records or chain id changing.
34: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms
34:
34: chain #res #atoms
34: 1 'A' 3 19
34: 2 'B' 3 28
34:
34: Reading residue database... (Charmm27)
34: Processing chain 1 'A' (19 atoms, 3 residues)
34: Identified residue ALA2 as a starting terminus.
34: Identified residue ASP4 as a ending terminus.
34: Start terminus ALA-2: NH3+
34: End terminus ASP-4: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 3 residues with 36 atoms
34: Chain time...
34: Processing chain 2 'B' (28 atoms, 3 residues)
34: Identified residue THR18 as a starting terminus.
34: Identified residue TRP20 as a ending terminus.
34: Start terminus THR-18: NH3+
34: End terminus TRP-20: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 3 residues with 57 atoms
34: Chain time...
34: Including chain 1 in system: 36 atoms 3 residues
34: Including chain 2 in system: 57 atoms 3 residues
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb.
34: The Charmm27 force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/2 (207 ms)
34: [ RUN ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/3
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
34: 8 out of 8 lines of specbond.dat converted successfully
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 35, now 35
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 83 pairs
34: Before cleaning: 83 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 1 cmap torsion pairs
34: There are 83 dihedrals, 6 impropers, 61 angles
34: 83 pairs, 35 bonds and 0 virtual sites
34: Total mass 306.314 a.m.u.
34: Total charge -1.000 e
34: Writing topology
34: 8 out of 8 lines of specbond.dat converted successfully
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 58, now 58
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 145 pairs
34: Before cleaning: 150 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 1 cmap torsion pairs
34: There are 150 dihedrals, 5 impropers, 103 angles
34: 142 pairs, 58 bonds and 0 virtual sites
34: Total mass 404.468 a.m.u.
34: Total charge -0.000 e
34: Writing topology
34: Now there are 93 atoms and 6 residues
34: Total mass in system 710.782 a.m.u.
34: Total charge in system -1.000 e
34:
34: Writing coordinate file...
34:
34: Using the Charmm27 force field in directory charmm27.ff
34:
34: going to rename charmm27.ff/aminoacids.r2b
34: going to rename charmm27.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb...
34: Read 'Fragments of peptides and ions', 47 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records and chain id changing.
34: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms
34:
34: chain #res #atoms
34: 1 'A' 3 19
34: 2 'B' 3 28
34:
34: Reading residue database... (Charmm27)
34: Processing chain 1 'A' (19 atoms, 3 residues)
34: Identified residue ALA2 as a starting terminus.
34: Identified residue ASP4 as a ending terminus.
34: Start terminus ALA-2: NH3+
34: End terminus ASP-4: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 3 residues with 36 atoms
34: Chain time...
34: Processing chain 2 'B' (28 atoms, 3 residues)
34: Identified residue THR18 as a starting terminus.
34: Identified residue TRP20 as a ending terminus.
34: Start terminus THR-18: NH3+
34: End terminus TRP-20: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 3 residues with 57 atoms
34: Chain time...
34: Including chain 1 in system: 36 atoms 3 residues
34: Including chain 2 in system: 57 atoms 3 residues
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb.
34: The Charmm27 force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/3 (205 ms)
34: [----------] 4 tests from ChainChanges/Pdb2gmxTest (830 ms total)
34:
34: [----------] Global test environment tear-down
34: [==========] 28 tests from 4 test cases ran. (11198 ms total)
34: [ PASSED ] 28 tests.
34/52 Test #34: Pdb2gmx3Test ........................ Passed 11.27 sec
test 35
Start 35: CorrelationsTest
35: Test command: /<<PKGBUILDDIR>>/build/basic/bin/correlations-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/CorrelationsTest.xml"
35: Test timeout computed to be: 30
35: [==========] Running 21 tests from 3 test cases.
35: [----------] Global test environment set-up.
35: [----------] 10 tests from AutocorrTest
35: [ RUN ] AutocorrTest.EacNormal
35: [ OK ] AutocorrTest.EacNormal (27 ms)
35: [ RUN ] AutocorrTest.EacNoNormalize
35: [ OK ] AutocorrTest.EacNoNormalize (17 ms)
35: [ RUN ] AutocorrTest.EacCos
35: [ OK ] AutocorrTest.EacCos (38 ms)
35: [ RUN ] AutocorrTest.EacVector
35: [ OK ] AutocorrTest.EacVector (41 ms)
35: [ RUN ] AutocorrTest.EacRcross
35: [ OK ] AutocorrTest.EacRcross (8 ms)
35: [ RUN ] AutocorrTest.EacP0
35: [ OK ] AutocorrTest.EacP0 (42 ms)
35: [ RUN ] AutocorrTest.EacP1
35: [ OK ] AutocorrTest.EacP1 (42 ms)
35: [ RUN ] AutocorrTest.EacP2
35: [ OK ] AutocorrTest.EacP2 (78 ms)
35: [ RUN ] AutocorrTest.EacP3
35: [ OK ] AutocorrTest.EacP3 (24 ms)
35: [ RUN ] AutocorrTest.EacP4
35: [ OK ] AutocorrTest.EacP4 (41 ms)
35: [----------] 10 tests from AutocorrTest (365 ms total)
35:
35: [----------] 1 test from ManyAutocorrelationTest
35: [ RUN ] ManyAutocorrelationTest.Empty
35: [ OK ] ManyAutocorrelationTest.Empty (1 ms)
35: [----------] 1 test from ManyAutocorrelationTest (1 ms total)
35:
35: [----------] 10 tests from ExpfitTest
35: [ RUN ] ExpfitTest.EffnEXP1
35: [ OK ] ExpfitTest.EffnEXP1 (5 ms)
35: [ RUN ] ExpfitTest.EffnEXP2
35: [ OK ] ExpfitTest.EffnEXP2 (6 ms)
35: [ RUN ] ExpfitTest.EffnEXPEXP
35: [ OK ] ExpfitTest.EffnEXPEXP (13 ms)
35: [ RUN ] ExpfitTest.EffnEXP5
35: [ OK ] ExpfitTest.EffnEXP5 (42 ms)
35: [ RUN ] ExpfitTest.EffnEXP7
35: [ OK ] ExpfitTest.EffnEXP7 (33 ms)
35: [ RUN ] ExpfitTest.EffnEXP9
35: [ OK ] ExpfitTest.EffnEXP9 (250 ms)
35: [ RUN ] ExpfitTest.EffnERF
35: [ OK ] ExpfitTest.EffnERF (18 ms)
35: [ RUN ] ExpfitTest.EffnERREST
35: [ OK ] ExpfitTest.EffnERREST (7 ms)
35: [ RUN ] ExpfitTest.EffnVAC
35: [ OK ] ExpfitTest.EffnVAC (46 ms)
35: [ RUN ] ExpfitTest.EffnPRES
35: [ OK ] ExpfitTest.EffnPRES (104 ms)
35: [----------] 10 tests from ExpfitTest (524 ms total)
35:
35: [----------] Global test environment tear-down
35: [==========] 21 tests from 3 test cases ran. (946 ms total)
35: [ PASSED ] 21 tests.
35/52 Test #35: CorrelationsTest .................... Passed 1.01 sec
test 36
Start 36: AnalysisDataUnitTests
36: Test command: /<<PKGBUILDDIR>>/build/basic/bin/analysisdata-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/AnalysisDataUnitTests.xml"
36: Test timeout computed to be: 30
36: [==========] Running 69 tests from 14 test cases.
36: [----------] Global test environment set-up.
36: [----------] 3 tests from AnalysisDataInitializationTest
36: [ RUN ] AnalysisDataInitializationTest.BasicInitialization
36: [ OK ] AnalysisDataInitializationTest.BasicInitialization (0 ms)
36: [ RUN ] AnalysisDataInitializationTest.ChecksMultiColumnModules
36: [ OK ] AnalysisDataInitializationTest.ChecksMultiColumnModules (0 ms)
36: [ RUN ] AnalysisDataInitializationTest.ChecksMultipointModules
36: [ OK ] AnalysisDataInitializationTest.ChecksMultipointModules (0 ms)
36: [----------] 3 tests from AnalysisDataInitializationTest (2 ms total)
36:
36: [----------] 8 tests from AnalysisDataCommonTest/0, where TypeParam = (anonymous namespace)::SimpleInputData
36: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectly
36: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectly (6 ms)
36: [ RUN ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly
36: [ OK ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly (3 ms)
36: [ RUN ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly
36: [ OK ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly (3 ms)
36: [ RUN ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly
36: [ OK ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly (3 ms)
36: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames
36: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames (4 ms)
36: [ RUN ] AnalysisDataCommonTest/0.FullStorageWorks
36: [ OK ] AnalysisDataCommonTest/0.FullStorageWorks (2 ms)
36: [ RUN ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData
36: [ OK ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData (2 ms)
36: [ RUN ] AnalysisDataCommonTest/0.LimitedStorageWorks
36: [ OK ] AnalysisDataCommonTest/0.LimitedStorageWorks (1 ms)
36: [----------] 8 tests from AnalysisDataCommonTest/0 (26 ms total)
36:
36: [----------] 8 tests from AnalysisDataCommonTest/1, where TypeParam = (anonymous namespace)::DataSetsInputData
36: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectly
36: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectly (3 ms)
36: [ RUN ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly
36: [ OK ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly (3 ms)
36: [ RUN ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly
36: [ OK ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly (4 ms)
36: [ RUN ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly
36: [ OK ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly (3 ms)
36: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames
36: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames (5 ms)
36: [ RUN ] AnalysisDataCommonTest/1.FullStorageWorks
36: [ OK ] AnalysisDataCommonTest/1.FullStorageWorks (2 ms)
36: [ RUN ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData
36: [ OK ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData (2 ms)
36: [ RUN ] AnalysisDataCommonTest/1.LimitedStorageWorks
36: [ OK ] AnalysisDataCommonTest/1.LimitedStorageWorks (2 ms)
36: [----------] 8 tests from AnalysisDataCommonTest/1 (26 ms total)
36:
36: [----------] 8 tests from AnalysisDataCommonTest/2, where TypeParam = (anonymous namespace)::MultipointInputData
36: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectly
36: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectly (4 ms)
36: [ RUN ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly
36: [ OK ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly (4 ms)
36: [ RUN ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly
36: [ OK ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly (4 ms)
36: [ RUN ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly
36: [ OK ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly (4 ms)
36: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames
36: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames (6 ms)
36: [ RUN ] AnalysisDataCommonTest/2.FullStorageWorks
36: [ OK ] AnalysisDataCommonTest/2.FullStorageWorks (2 ms)
36: [ RUN ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData
36: [ OK ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData (2 ms)
36: [ RUN ] AnalysisDataCommonTest/2.LimitedStorageWorks
36: [ OK ] AnalysisDataCommonTest/2.LimitedStorageWorks (2 ms)
36: [----------] 8 tests from AnalysisDataCommonTest/2 (31 ms total)
36:
36: [----------] 8 tests from AnalysisDataCommonTest/3, where TypeParam = (anonymous namespace)::MultipointDataSetsInputData
36: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectly
36: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectly (4 ms)
36: [ RUN ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly
36: [ OK ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly (4 ms)
36: [ RUN ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly
36: [ OK ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly (4 ms)
36: [ RUN ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly
36: [ OK ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly (4 ms)
36: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames
36: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames (6 ms)
36: [ RUN ] AnalysisDataCommonTest/3.FullStorageWorks
36: [ OK ] AnalysisDataCommonTest/3.FullStorageWorks (3 ms)
36: [ RUN ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData
36: [ OK ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData (2 ms)
36: [ RUN ] AnalysisDataCommonTest/3.LimitedStorageWorks
36: [ OK ] AnalysisDataCommonTest/3.LimitedStorageWorks (2 ms)
36: [----------] 8 tests from AnalysisDataCommonTest/3 (31 ms total)
36:
36: [----------] 4 tests from AnalysisArrayDataTest
36: [ RUN ] AnalysisArrayDataTest.CallsModuleCorrectly
36: [ OK ] AnalysisArrayDataTest.CallsModuleCorrectly (3 ms)
36: [ RUN ] AnalysisArrayDataTest.StorageWorks
36: [ OK ] AnalysisArrayDataTest.StorageWorks (2 ms)
36: [ RUN ] AnalysisArrayDataTest.CanSetXAxis
36: [ OK ] AnalysisArrayDataTest.CanSetXAxis (0 ms)
36: [ RUN ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount
36: [ OK ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount (0 ms)
36: [----------] 4 tests from AnalysisArrayDataTest (7 ms total)
36:
36: [----------] 6 tests from AverageModuleTest
36: [ RUN ] AverageModuleTest.BasicTest
36: [ OK ] AverageModuleTest.BasicTest (25 ms)
36: [ RUN ] AverageModuleTest.HandlesMultipointData
36: [ OK ] AverageModuleTest.HandlesMultipointData (6 ms)
36: [ RUN ] AverageModuleTest.HandlesMultipleDataSets
36: [ OK ] AverageModuleTest.HandlesMultipleDataSets (6 ms)
36: [ RUN ] AverageModuleTest.HandlesDataSetAveraging
36: [ OK ] AverageModuleTest.HandlesDataSetAveraging (6 ms)
36: [ RUN ] AverageModuleTest.CanCustomizeXAxis
36: [ OK ] AverageModuleTest.CanCustomizeXAxis (5 ms)
36: [ RUN ] AverageModuleTest.CanCustomizeNonUniformXAxis
36: [ OK ] AverageModuleTest.CanCustomizeNonUniformXAxis (5 ms)
36: [----------] 6 tests from AverageModuleTest (54 ms total)
36:
36: [----------] 2 tests from FrameAverageModuleTest
36: [ RUN ] FrameAverageModuleTest.BasicTest
36: [ OK ] FrameAverageModuleTest.BasicTest (4 ms)
36: [ RUN ] FrameAverageModuleTest.HandlesMultipleDataSets
36: [ OK ] FrameAverageModuleTest.HandlesMultipleDataSets (6 ms)
36: [----------] 2 tests from FrameAverageModuleTest (12 ms total)
36:
36: [----------] 7 tests from AnalysisHistogramSettingsTest
36: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBins
36: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBins (0 ms)
36: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins
36: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins (0 ms)
36: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount
36: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount (0 ms)
36: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth
36: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth (0 ms)
36: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins
36: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins (0 ms)
36: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins
36: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins (0 ms)
36: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange
36: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange (0 ms)
36: [----------] 7 tests from AnalysisHistogramSettingsTest (2 ms total)
36:
36: [----------] 2 tests from SimpleHistogramModuleTest
36: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectly
36: [ OK ] SimpleHistogramModuleTest.ComputesCorrectly (7 ms)
36: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll
36: [ OK ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll (7 ms)
36: [----------] 2 tests from SimpleHistogramModuleTest (15 ms total)
36:
36: [----------] 3 tests from WeightedHistogramModuleTest
36: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectly
36: [ OK ] WeightedHistogramModuleTest.ComputesCorrectly (7 ms)
36: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll
36: [ OK ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll (8 ms)
36: [ RUN ] WeightedHistogramModuleTest.HandlesMultipleDataSets
36: [ OK ] WeightedHistogramModuleTest.HandlesMultipleDataSets (8 ms)
36: [----------] 3 tests from WeightedHistogramModuleTest (25 ms total)
36:
36: [----------] 3 tests from BinAverageModuleTest
36: [ RUN ] BinAverageModuleTest.ComputesCorrectly
36: [ OK ] BinAverageModuleTest.ComputesCorrectly (6 ms)
36: [ RUN ] BinAverageModuleTest.ComputesCorrectlyWithAll
36: [ OK ] BinAverageModuleTest.ComputesCorrectlyWithAll (7 ms)
36: [ RUN ] BinAverageModuleTest.HandlesMultipleDataSets
36: [ OK ] BinAverageModuleTest.HandlesMultipleDataSets (6 ms)
36: [----------] 3 tests from BinAverageModuleTest (20 ms total)
36:
36: [----------] 4 tests from AbstractAverageHistogramTest
36: [ RUN ] AbstractAverageHistogramTest.ClonesCorrectly
36: [ OK ] AbstractAverageHistogramTest.ClonesCorrectly (9 ms)
36: [ RUN ] AbstractAverageHistogramTest.ComputesCumulativeHistogram
36: [ OK ] AbstractAverageHistogramTest.ComputesCumulativeHistogram (8 ms)
36: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth
36: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth (7 ms)
36: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins
36: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins (7 ms)
36: [----------] 4 tests from AbstractAverageHistogramTest (32 ms total)
36:
36: [----------] 3 tests from LifetimeModuleTest
36: [ RUN ] LifetimeModuleTest.BasicTest
36: [ OK ] LifetimeModuleTest.BasicTest (5 ms)
36: [ RUN ] LifetimeModuleTest.CumulativeTest
36: [ OK ] LifetimeModuleTest.CumulativeTest (5 ms)
36: [ RUN ] LifetimeModuleTest.HandlesMultipleDataSets
36: [ OK ] LifetimeModuleTest.HandlesMultipleDataSets (6 ms)
36: [----------] 3 tests from LifetimeModuleTest (16 ms total)
36:
36: [----------] Global test environment tear-down
36: [==========] 69 tests from 14 test cases ran. (303 ms total)
36: [ PASSED ] 69 tests.
36/52 Test #36: AnalysisDataUnitTests ............... Passed 0.38 sec
test 37
Start 37: CoordinateIOTests
37: Test command: /<<PKGBUILDDIR>>/build/basic/bin/coordinateio-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/CoordinateIOTests.xml"
37: Test timeout computed to be: 30
37: [==========] Running 64 tests from 19 test cases.
37: [----------] Global test environment set-up.
37: [----------] 1 test from OutputSelectorDeathTest
37: [ RUN ] OutputSelectorDeathTest.RejectsBadSelection
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] OutputSelectorDeathTest.RejectsBadSelection (34 ms)
37: [----------] 1 test from OutputSelectorDeathTest (35 ms total)
37:
37: [----------] 5 tests from TrajectoryFrameWriterTest
37: [ RUN ] TrajectoryFrameWriterTest.RejectsWrongFiletype
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] TrajectoryFrameWriterTest.RejectsWrongFiletype (23 ms)
37: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms (23 ms)
37: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms (22 ms)
37: [ RUN ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms (45 ms)
37: [ RUN ] TrajectoryFrameWriterTest.TNGOutputWorks
37: [ OK ] TrajectoryFrameWriterTest.TNGOutputWorks (0 ms)
37: [----------] 5 tests from TrajectoryFrameWriterTest (113 ms total)
37:
37: [----------] 5 tests from OutputAdapterContainer
37: [ RUN ] OutputAdapterContainer.MakeEmpty
37: [ OK ] OutputAdapterContainer.MakeEmpty (0 ms)
37: [ RUN ] OutputAdapterContainer.AddAdapter
37: [ OK ] OutputAdapterContainer.AddAdapter (0 ms)
37: [ RUN ] OutputAdapterContainer.RejectBadAdapter
37: [ OK ] OutputAdapterContainer.RejectBadAdapter (0 ms)
37: [ RUN ] OutputAdapterContainer.RejectDuplicateAdapter
37: [ OK ] OutputAdapterContainer.RejectDuplicateAdapter (0 ms)
37: [ RUN ] OutputAdapterContainer.AcceptMultipleAdapters
37: [ OK ] OutputAdapterContainer.AcceptMultipleAdapters (1 ms)
37: [----------] 5 tests from OutputAdapterContainer (1 ms total)
37:
37: [----------] 5 tests from FlagTest
37: [ RUN ] FlagTest.CanSetSimpleFlag
37: [ OK ] FlagTest.CanSetSimpleFlag (0 ms)
37: [ RUN ] FlagTest.CanAddNewBox
37: [ OK ] FlagTest.CanAddNewBox (0 ms)
37: [ RUN ] FlagTest.SetsImplicitPrecisionChange
37: [ OK ] FlagTest.SetsImplicitPrecisionChange (0 ms)
37: [ RUN ] FlagTest.SetsImplicitStartTimeChange
37: [ OK ] FlagTest.SetsImplicitStartTimeChange (0 ms)
37: [ RUN ] FlagTest.SetsImplicitTimeStepChange
37: [ OK ] FlagTest.SetsImplicitTimeStepChange (0 ms)
37: [----------] 5 tests from FlagTest (1 ms total)
37:
37: [----------] 5 tests from SetAtomsTest
37: [ RUN ] SetAtomsTest.RemovesExistingAtoms
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] SetAtomsTest.RemovesExistingAtoms (23 ms)
37: [ RUN ] SetAtomsTest.AddsNewAtoms
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] SetAtomsTest.AddsNewAtoms (22 ms)
37: [ RUN ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable (23 ms)
37: [ RUN ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable (22 ms)
37: [ RUN ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible (23 ms)
37: [----------] 5 tests from SetAtomsTest (113 ms total)
37:
37: [----------] 2 tests from SetBothTimeTest
37: [ RUN ] SetBothTimeTest.StartTimeZeroWorks
37: [ OK ] SetBothTimeTest.StartTimeZeroWorks (0 ms)
37: [ RUN ] SetBothTimeTest.SetStartTimeNonZeroWorks
37: [ OK ] SetBothTimeTest.SetStartTimeNonZeroWorks (0 ms)
37: [----------] 2 tests from SetBothTimeTest (0 ms total)
37:
37: [----------] 2 tests from SetStartTimeTest
37: [ RUN ] SetStartTimeTest.WorksWithNonZeroStart
37: [ OK ] SetStartTimeTest.WorksWithNonZeroStart (0 ms)
37: [ RUN ] SetStartTimeTest.WorksWithZeroStart
37: [ OK ] SetStartTimeTest.WorksWithZeroStart (1 ms)
37: [----------] 2 tests from SetStartTimeTest (1 ms total)
37:
37: [----------] 1 test from SetTimeStepTest
37: [ RUN ] SetTimeStepTest.SetTimeStepWorks
37: [ OK ] SetTimeStepTest.SetTimeStepWorks (0 ms)
37: [----------] 1 test from SetTimeStepTest (0 ms total)
37:
37: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest
37: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0 (22 ms)
37: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1 (23 ms)
37: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2 (22 ms)
37: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3 (23 ms)
37: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4 (22 ms)
37: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5 (22 ms)
37: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest (135 ms total)
37:
37: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles
37: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/0
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/0 (22 ms)
37: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/1
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/1 (22 ms)
37: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/2
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/2 (22 ms)
37: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles (67 ms total)
37:
37: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles
37: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0
37: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0 (0 ms)
37: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1
37: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1 (1 ms)
37: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2
37: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2 (0 ms)
37: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles (1 ms total)
37:
37: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles
37: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/0
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/0 (46 ms)
37: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/1
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/1 (46 ms)
37: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/2
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/2 (46 ms)
37: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/3
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/3 (46 ms)
37: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles (184 ms total)
37:
37: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles
37: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/0
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/0 (23 ms)
37: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/1
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/1 (22 ms)
37: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/2
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/2 (22 ms)
37: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles (68 ms total)
37:
37: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles
37: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0
37: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0 (0 ms)
37: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1
37: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1 (0 ms)
37: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2
37: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2 (0 ms)
37: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles (2 ms total)
37:
37: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles
37: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/0
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/0 (22 ms)
37: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/1
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/1 (22 ms)
37: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles (45 ms total)
37:
37: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles
37: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0
37: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0 (0 ms)
37: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1
37: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1 (0 ms)
37: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2
37: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2 (0 ms)
37: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3
37: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3 (0 ms)
37: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles (1 ms total)
37:
37: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles
37: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/0
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/0 (22 ms)
37: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/1
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/1 (22 ms)
37: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles (45 ms total)
37:
37: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles
37: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0
37: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0 (1 ms)
37: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1
37: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1 (0 ms)
37: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2
37: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2 (1 ms)
37: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3
37: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3 (0 ms)
37: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles (2 ms total)
37:
37: [----------] 4 tests from ModuleSupported/NoOptionalOutput
37: [ RUN ] ModuleSupported/NoOptionalOutput.Works/0
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] ModuleSupported/NoOptionalOutput.Works/0 (22 ms)
37: [ RUN ] ModuleSupported/NoOptionalOutput.Works/1
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] ModuleSupported/NoOptionalOutput.Works/1 (22 ms)
37: [ RUN ] ModuleSupported/NoOptionalOutput.Works/2
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] ModuleSupported/NoOptionalOutput.Works/2 (22 ms)
37: [ RUN ] ModuleSupported/NoOptionalOutput.Works/3
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] ModuleSupported/NoOptionalOutput.Works/3 (22 ms)
37: [----------] 4 tests from ModuleSupported/NoOptionalOutput (91 ms total)
37:
37: [----------] Global test environment tear-down
37: [==========] 64 tests from 19 test cases ran. (907 ms total)
37: [ PASSED ] 64 tests.
37/52 Test #37: CoordinateIOTests ................... Passed 0.98 sec
test 38
Start 38: TrajectoryAnalysisUnitTests
38: Test command: /<<PKGBUILDDIR>>/build/basic/bin/trajectoryanalysis-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/TrajectoryAnalysisUnitTests.xml"
38: Test timeout computed to be: 30
38: [==========] Running 80 tests from 16 test cases.
38: [----------] Global test environment set-up.
38: [----------] 5 tests from ClustsizeTest
38: [ RUN ] ClustsizeTest.NoMolDefaultCutoff
38: Reading frames from pdb file
Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements
38: There is one group in the index
38: '', 24 atoms
38:
Reading frame 1 time 0.000
Last frame 1 time 0.000
38: Total number of atoms in clusters = 24
38: cmid: 2, cmax: 4, max_size: 6
38: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6
38: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolDefaultCutoff (30 ms)
38: [ RUN ] ClustsizeTest.NoMolShortCutoff
38: Reading frames from pdb file
Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements
38: There is one group in the index
38: '', 24 atoms
38:
Reading frame 1 time 0.000
Last frame 1 time 0.000
38: Total number of atoms in clusters = 24
38: cmid: 1, cmax: 6, max_size: 6
38: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6
38: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolShortCutoff (11 ms)
38: [ RUN ] ClustsizeTest.MolDefaultCutoff
38: Reading frames from pdb file
Reading frame 0 time 0.000 Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
38: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
38: '', 24 atoms
38:
Reading frame 1 time 0.000
Last frame 1 time 0.000
38: Total number of atoms in clusters = 8
38: cmid: 2, cmax: 4, max_size: 2
38: 50%100%cmid: 2, cmax: 6, max_size: 2
38: 50%100%[ OK ] ClustsizeTest.MolDefaultCutoff (16 ms)
38: [ RUN ] ClustsizeTest.MolShortCutoff
38: Reading frames from pdb file
Reading frame 0 time 0.000 Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
38: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
38: '', 24 atoms
38:
Reading frame 1 time 0.000
Last frame 1 time 0.000
38: Total number of atoms in clusters = 8
38: cmid: 1, cmax: 6, max_size: 2
38: 50%100%cmid: 2, cmax: 6, max_size: 2
38: 50%100%[ OK ] ClustsizeTest.MolShortCutoff (13 ms)
38: [ RUN ] ClustsizeTest.MolCSize
38: Reading frames from pdb file
Reading frame 0 time 0.000 Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
38: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
38: '', 24 atoms
38:
Reading frame 1 time 0.000
Last frame 1 time 0.000
38: Total number of atoms in clusters = 8
38: cmid: 2, cmax: 4, max_size: 2
38: 50%100%cmid: 2, cmax: 6, max_size: 2
38: 50%100%[ OK ] ClustsizeTest.MolCSize (15 ms)
38: [----------] 5 tests from ClustsizeTest (85 ms total)
38:
38: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest
38: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp
38: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp (14 ms)
38: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory
38: Reading frames from gro file 'Test system', 8 atoms.
38:
Reading frame 0 time 0.000
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38:
Reading frame 1 time 0.000
Last frame 1 time 0.000
38: Analyzed 2 frames, last time 0.000
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory (17 ms)
38: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset
38: Reading frames from gro file 'Test system', 8 atoms.
38:
Reading frame 0 time 0.000
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset (16 ms)
38: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory
38: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory (2 ms)
38: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest (49 ms total)
38:
38: [----------] 11 tests from AngleModuleTest
38: [ RUN ] AngleModuleTest.ComputesSimpleAngles
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] AngleModuleTest.ComputesSimpleAngles (27 ms)
38: [ RUN ] AngleModuleTest.ComputesDihedrals
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] AngleModuleTest.ComputesDihedrals (18 ms)
38: [ RUN ] AngleModuleTest.ComputesVectorPairAngles
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] AngleModuleTest.ComputesVectorPairAngles (19 ms)
38: [ RUN ] AngleModuleTest.ComputesVectorPlanePairAngles
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] AngleModuleTest.ComputesVectorPlanePairAngles (18 ms)
38: [ RUN ] AngleModuleTest.ComputesPlaneZAxisAngles
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] AngleModuleTest.ComputesPlaneZAxisAngles (19 ms)
38: [ RUN ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles (18 ms)
38: [ RUN ] AngleModuleTest.ComputesVectorTimeZeroAngles
38: Reading frames from gro file 'Test system for different angles', 33 atoms.
38:
Reading frame 0 time 0.000
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38:
Reading frame 1 time 0.000
Last frame 1 time 0.000
38: Analyzed 2 frames, last time 0.000
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] AngleModuleTest.ComputesVectorTimeZeroAngles (23 ms)
38: [ RUN ] AngleModuleTest.ComputesMultipleAngles
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] AngleModuleTest.ComputesMultipleAngles (20 ms)
38: [ RUN ] AngleModuleTest.HandlesDynamicSelections
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] AngleModuleTest.HandlesDynamicSelections (18 ms)
38: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorAngles
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorAngles (19 ms)
38: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles (20 ms)
38: [----------] 11 tests from AngleModuleTest (222 ms total)
38:
38: [----------] 4 tests from ConvertTrjModuleTest
38: [ RUN ] ConvertTrjModuleTest.WritesNormalOutput
38: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
38: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
38:
Reading frame 0 time 0.000
Last frame 0 time 0.000
38: Analyzed 1 frames, last time 0.000
38: [ OK ] ConvertTrjModuleTest.WritesNormalOutput (62 ms)
38: [ RUN ] ConvertTrjModuleTest.WritesAtomSubset
38: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
38: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
38:
Reading frame 0 time 0.000
Last frame 0 time 0.000
38: Analyzed 1 frames, last time 0.000
38: [ OK ] ConvertTrjModuleTest.WritesAtomSubset (55 ms)
38: [ RUN ] ConvertTrjModuleTest.WorksWithAtomAdding
38: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
38: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
38: Reading frames from pdb file
Reading frame 0 time 0.000 '', 24 atoms
38:
Reading frame 1 time 0.000
Last frame 1 time 0.000
38: Analyzed 2 frames, last time 0.000
38: [ OK ] ConvertTrjModuleTest.WorksWithAtomAdding (12 ms)
38: [ RUN ] ConvertTrjModuleTest.WorksWithAtomsAndSelection
38: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
38: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
38: Reading frames from pdb file
Reading frame 0 time 0.000 '', 24 atoms
38:
Reading frame 1 time 0.000
Last frame 1 time 0.000
38: Analyzed 2 frames, last time 0.000
38: [ OK ] ConvertTrjModuleTest.WorksWithAtomsAndSelection (10 ms)
38: [----------] 4 tests from ConvertTrjModuleTest (141 ms total)
38:
38: [----------] 3 tests from DistanceModuleTest
38: [ RUN ] DistanceModuleTest.ComputesDistances
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: atomname S1 S2:
38: Number of samples: 5
38: Average distance: 1.43246 nm
38: Standard deviation: 0.96700 nm
38: [ OK ] DistanceModuleTest.ComputesDistances (23 ms)
38: [ RUN ] DistanceModuleTest.ComputesMultipleDistances
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: atomname S1 S2:
38: Number of samples: 5
38: Average distance: 1.43246 nm
38: Standard deviation: 0.96700 nm
38: resindex 1 to 4 and atomname CB merge resindex 2 to 5 and atomname CB:
38: Number of samples: 4
38: Average distance: 1.81066 nm
38: Standard deviation: 0.79289 nm
38: [ OK ] DistanceModuleTest.ComputesMultipleDistances (25 ms)
38: [ RUN ] DistanceModuleTest.HandlesDynamicSelections
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: atomname S1 S2 and res_cog x < 2.8:
38: Number of samples: 3
38: Average distance: 1.72076 nm
38: Standard deviation: 1.24839 nm
38: [ OK ] DistanceModuleTest.HandlesDynamicSelections (24 ms)
38: [----------] 3 tests from DistanceModuleTest (75 ms total)
38:
38: [----------] 2 tests from ExtractClusterModuleTest
38: [ RUN ] ExtractClusterModuleTest.WorksWithAllAtoms
38: trr version: GMX_trn_file (single precision)
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.002
Reading frame 2 time 0.004
Reading frame 3 time 0.006
Reading frame 4 time 0.008
Reading frame 5 time 0.010
Reading frame 6 time 0.012
Reading frame 7 time 0.014
Reading frame 8 time 0.016
Reading frame 9 time 0.018
Reading frame 10 time 0.020
Reading frame 11 time 0.022
Reading frame 12 time 0.024
Reading frame 13 time 0.026
Reading frame 14 time 0.028
Reading frame 15 time 0.030
Reading frame 16 time 0.032
Reading frame 17 time 0.034
Reading frame 18 time 0.036
Reading frame 19 time 0.038
Reading frame 20 time 0.040
38: Analyzed 26 frames, last time 0.050
38: There are 8 clusters containing 26 structures, highest framenr is 25
38: [ OK ] ExtractClusterModuleTest.WorksWithAllAtoms (19 ms)
38: [ RUN ] ExtractClusterModuleTest.WorksWithAtomSubset
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.002
Reading frame 2 time 0.004
Reading frame 3 time 0.006
Reading frame 4 time 0.008
Reading frame 5 time 0.010
Reading frame 6 time 0.012
Reading frame 7 time 0.014
Reading frame 8 time 0.016
Reading frame 9 time 0.018
Reading frame 10 time 0.020
Reading frame 11 time 0.022
Reading frame 12 time 0.024
Reading frame 13 time 0.026
Reading frame 14 time 0.028
Reading frame 15 time 0.030
Reading frame 16 time 0.032
Reading frame 17 time 0.034
Reading frame 18 time 0.036
Reading frame 19 time 0.038
Reading frame 20 time 0.040
38: Analyzed 26 frames, last time 0.050
38: There are 8 clusters containing 26 structures, highest framenr is 25
38: [ OK ] ExtractClusterModuleTest.WorksWithAtomSubset (14 ms)
38: [----------] 2 tests from ExtractClusterModuleTest (34 ms total)
38:
38: [----------] 2 tests from FreeVolumeModuleTest
38: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolume
38: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
38: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
38: from the source below. This means the results may be different
38: compared to previous GROMACS versions.
38:
38: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
38: A. Bondi
38: van der Waals Volumes and Radii
38: J. Phys. Chem. 68 (1964) pp. 441-451
38: -------- -------- --- Thank You --- -------- --------
38:
38: Could not determine VDW radius for CO2-RM. Set to zero.
38: Could not determine VDW radius for CO2-RM. Set to zero.
38: Could not determine VDW radius for CO2-RM. Set to zero.
38: Could not determine VDW radius for CO2-RM. Set to zero.
38: Could not determine VDW radius for CO2-RM. Set to zero.
38: Could not determine VDW radius for CO2-RM. Set to zero.
38: Could not determine VDW radius for CO2-RM. Set to zero.
38: Could not determine VDW radius for CO2-RM. Set to zero.
38: Could not determine VDW radius for CO2-RM. Set to zero.
38: Could not determine VDW radius for 40 particles. These were set to zero.
38:
Reading frame 0 time 0.000
Last frame 0 time 0.000
38: Analyzed 1 frames, last time 0.000
38: cutoff = 0.18 nm
38: probe_radius = 0 nm
38: seed = 13
38: ninsert = 1000 probes per nm^3
38:
38: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
38: A. Bondi
38: van der Waals Volumes and Radii
38: J. Phys. Chem. 68 (1964) pp. 441-451
38: -------- -------- --- Thank You --- -------- --------
38:
38:
38: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
38: Tuanan C. Lourenco and Mariny F. C. Coelho and Teodorico C. Ramalho and David
38: van der Spoel and Luciano T. Costa
38: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium
38: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View
38: Environ. Sci. Technol. 47 (2013) pp. 7421-7429
38: -------- -------- --- Thank You --- -------- --------
38:
38: Free volume 38.02 +/- 0.00 %
38: Total volume 68.92 +/- 0.00 nm^3
38: Number of molecules 340 total mass 63491.38 Dalton
38: Average molar mass: 186.74 Dalton
38: Density rho: 1529.71 +/- 0.00 nm^3
38: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3
38: Molecular van der Waals volume assuming homogeneity: 0.1256 +/- 0.0000 nm^3
38: Fractional free volume 0.194 +/- 0.000
38: [ OK ] FreeVolumeModuleTest.ComputesFreeVolume (645 ms)
38: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolumeSelection
38: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
38: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
38: from the source below. This means the results may be different
38: compared to previous GROMACS versions.
38:
38: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
38: A. Bondi
38: van der Waals Volumes and Radii
38: J. Phys. Chem. 68 (1964) pp. 441-451
38: -------- -------- --- Thank You --- -------- --------
38:
38:
Reading frame 0 time 0.000
Last frame 0 time 0.000
38: Analyzed 1 frames, last time 0.000
38: cutoff = 0.18 nm
38: probe_radius = 0 nm
38: seed = 17
38: ninsert = 1000 probes per nm^3
38:
38: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
38: A. Bondi
38: van der Waals Volumes and Radii
38: J. Phys. Chem. 68 (1964) pp. 441-451
38: -------- -------- --- Thank You --- -------- --------
38:
38:
38: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
38: Tuanan C. Lourenco and Mariny F. C. Coelho and Teodorico C. Ramalho and David
38: van der Spoel and Luciano T. Costa
38: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium
38: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View
38: Environ. Sci. Technol. 47 (2013) pp. 7421-7429
38: -------- -------- --- Thank You --- -------- --------
38:
38: Free volume 38.48 +/- 0.00 %
38: Total volume 68.92 +/- 0.00 nm^3
38: Number of molecules 340 total mass 63491.38 Dalton
38: Average molar mass: 186.74 Dalton
38: Density rho: 1529.71 +/- 0.00 nm^3
38: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3
38: Molecular van der Waals volume assuming homogeneity: 0.1247 +/- 0.0000 nm^3
38: Fractional free volume 0.200 +/- 0.000
38: [ OK ] FreeVolumeModuleTest.ComputesFreeVolumeSelection (641 ms)
38: [----------] 2 tests from FreeVolumeModuleTest (1287 ms total)
38:
38: [----------] 7 tests from PairDistanceModuleTest
38: [ RUN ] PairDistanceModuleTest.ComputesAllDistances
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] PairDistanceModuleTest.ComputesAllDistances (19 ms)
38: [ RUN ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff (19 ms)
38: [ RUN ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff (18 ms)
38: [ RUN ] PairDistanceModuleTest.ComputesMaxDistance
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] PairDistanceModuleTest.ComputesMaxDistance (17 ms)
38: [ RUN ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff (18 ms)
38: [ RUN ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff (18 ms)
38: [ RUN ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff (18 ms)
38: [----------] 7 tests from PairDistanceModuleTest (128 ms total)
38:
38: [----------] 5 tests from RdfModuleTest
38: [ RUN ] RdfModuleTest.BasicTest
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] RdfModuleTest.BasicTest (151 ms)
38: [ RUN ] RdfModuleTest.SelectionsSolelyFromIndexFileWork
38: Reading frames from gro file '216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984', 648 atoms.
38:
Reading frame 0 time 0.000
Last frame 0 time 0.000
38: Analyzed 1 frames, last time 0.000
38: [ OK ] RdfModuleTest.SelectionsSolelyFromIndexFileWork (101 ms)
38: [ RUN ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork (152 ms)
38: [ RUN ] RdfModuleTest.CalculatesSurf
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] RdfModuleTest.CalculatesSurf (90 ms)
38: [ RUN ] RdfModuleTest.CalculatesXY
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] RdfModuleTest.CalculatesXY (174 ms)
38: [----------] 5 tests from RdfModuleTest (671 ms total)
38:
38: [----------] 5 tests from SasaModuleTest
38: [ RUN ] SasaModuleTest.BasicTest
38:
38: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
38: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
38: Michael Scharf
38: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
38: of Surface Area and Volume and to Dot Surface Contouring of Molecular
38: Assemblies
38: J. Comp. Chem. 16 (1995) pp. 273-284
38: -------- -------- --- Thank You --- -------- --------
38:
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
38: from the source below. This means the results may be different
38: compared to previous GROMACS versions.
38:
38: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
38: A. Bondi
38: van der Waals Volumes and Radii
38: J. Phys. Chem. 68 (1964) pp. 441-451
38: -------- -------- --- Thank You --- -------- --------
38:
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38: [ OK ] SasaModuleTest.BasicTest (78 ms)
38: [ RUN ] SasaModuleTest.HandlesSelectedResidues
38:
38: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
38: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
38: Michael Scharf
38: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
38: of Surface Area and Volume and to Dot Surface Contouring of Molecular
38: Assemblies
38: J. Comp. Chem. 16 (1995) pp. 273-284
38: -------- -------- --- Thank You --- -------- --------
38:
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
38: from the source below. This means the results may be different
38: compared to previous GROMACS versions.
38:
38: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
38: A. Bondi
38: van der Waals Volumes and Radii
38: J. Phys. Chem. 68 (1964) pp. 441-451
38: -------- -------- --- Thank You --- -------- --------
38:
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38: [ OK ] SasaModuleTest.HandlesSelectedResidues (48 ms)
38: [ RUN ] SasaModuleTest.WritesConnollySurfaceWithSolute
38:
38: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
38: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
38: Michael Scharf
38: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
38: of Surface Area and Volume and to Dot Surface Contouring of Molecular
38: Assemblies
38: J. Comp. Chem. 16 (1995) pp. 273-284
38: -------- -------- --- Thank You --- -------- --------
38:
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
38: from the source below. This means the results may be different
38: compared to previous GROMACS versions.
38:
38: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
38: A. Bondi
38: van der Waals Volumes and Radii
38: J. Phys. Chem. 68 (1964) pp. 441-451
38: -------- -------- --- Thank You --- -------- --------
38:
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38: [ OK ] SasaModuleTest.WritesConnollySurfaceWithSolute (42 ms)
38: [ RUN ] SasaModuleTest.HandlesDynamicOutputGroup
38:
38: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
38: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
38: Michael Scharf
38: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
38: of Surface Area and Volume and to Dot Surface Contouring of Molecular
38: Assemblies
38: J. Comp. Chem. 16 (1995) pp. 273-284
38: -------- -------- --- Thank You --- -------- --------
38:
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
38: from the source below. This means the results may be different
38: compared to previous GROMACS versions.
38:
38: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
38: A. Bondi
38: van der Waals Volumes and Radii
38: J. Phys. Chem. 68 (1964) pp. 441-451
38: -------- -------- --- Thank You --- -------- --------
38:
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38: [ OK ] SasaModuleTest.HandlesDynamicOutputGroup (57 ms)
38: [ RUN ] SasaModuleTest.HandlesDynamicCalculationGroup
38:
38: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
38: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
38: Michael Scharf
38: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
38: of Surface Area and Volume and to Dot Surface Contouring of Molecular
38: Assemblies
38: J. Comp. Chem. 16 (1995) pp. 273-284
38: -------- -------- --- Thank You --- -------- --------
38:
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
38: from the source below. This means the results may be different
38: compared to previous GROMACS versions.
38:
38: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
38: A. Bondi
38: van der Waals Volumes and Radii
38: J. Phys. Chem. 68 (1964) pp. 441-451
38: -------- -------- --- Thank You --- -------- --------
38:
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38: [ OK ] SasaModuleTest.HandlesDynamicCalculationGroup (55 ms)
38: [----------] 5 tests from SasaModuleTest (290 ms total)
38:
38: [----------] 8 tests from SelectModuleTest
38: [ RUN ] SelectModuleTest.BasicTest
38: Reading frames from gro file 'Test system', 15 atoms.
38:
Reading frame 0 time 0.000
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38:
Reading frame 1 time 0.000
Last frame 1 time 0.000
38: Analyzed 2 frames, last time 0.000
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] SelectModuleTest.BasicTest (33 ms)
38: [ RUN ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput
38: Reading frames from gro file 'Test system', 15 atoms.
38:
Reading frame 0 time 0.000
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38:
Reading frame 1 time 0.000
Last frame 1 time 0.000
38: Analyzed 2 frames, last time 0.000
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput (25 ms)
38: [ RUN ] SelectModuleTest.HandlesPDBOutputWithPDBInput
38: Reading frames from gro file 'Test system', 15 atoms.
38:
Reading frame 0 time 0.000
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38:
Reading frame 1 time 0.000
Last frame 1 time 0.000
38: Analyzed 2 frames, last time 0.000
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] SelectModuleTest.HandlesPDBOutputWithPDBInput (25 ms)
38: [ RUN ] SelectModuleTest.HandlesMaxPDBOutput
38: Reading frames from gro file 'Test system', 15 atoms.
38:
Reading frame 0 time 0.000
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38:
Reading frame 1 time 0.000
Last frame 1 time 0.000
38: Analyzed 2 frames, last time 0.000
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] SelectModuleTest.HandlesMaxPDBOutput (25 ms)
38: [ RUN ] SelectModuleTest.HandlesSelectedPDBOutput
38: Reading frames from gro file 'Test system', 15 atoms.
38:
Reading frame 0 time 0.000
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38:
Reading frame 1 time 0.000
Last frame 1 time 0.000
38: Analyzed 2 frames, last time 0.000
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] SelectModuleTest.HandlesSelectedPDBOutput (25 ms)
38: [ RUN ] SelectModuleTest.NormalizesSizes
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] SelectModuleTest.NormalizesSizes (17 ms)
38: [ RUN ] SelectModuleTest.WritesResidueNumbers
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] SelectModuleTest.WritesResidueNumbers (16 ms)
38: [ RUN ] SelectModuleTest.WritesResidueIndices
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] SelectModuleTest.WritesResidueIndices (18 ms)
38: [----------] 8 tests from SelectModuleTest (186 ms total)
38:
38: [----------] 10 tests from SurfaceAreaTest
38: [ RUN ] SurfaceAreaTest.ComputesSinglePoint
38: [ OK ] SurfaceAreaTest.ComputesSinglePoint (1 ms)
38: [ RUN ] SurfaceAreaTest.ComputesTwoPoints
38: [ OK ] SurfaceAreaTest.ComputesTwoPoints (6 ms)
38: [ RUN ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius
38: [ OK ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius (6 ms)
38: [ RUN ] SurfaceAreaTest.SurfacePoints12
38: [ OK ] SurfaceAreaTest.SurfacePoints12 (1 ms)
38: [ RUN ] SurfaceAreaTest.SurfacePoints32
38: [ OK ] SurfaceAreaTest.SurfacePoints32 (2 ms)
38: [ RUN ] SurfaceAreaTest.SurfacePoints42
38: [ OK ] SurfaceAreaTest.SurfacePoints42 (3 ms)
38: [ RUN ] SurfaceAreaTest.SurfacePoints122
38: [ OK ] SurfaceAreaTest.SurfacePoints122 (6 ms)
38: [ RUN ] SurfaceAreaTest.Computes100Points
38: [ OK ] SurfaceAreaTest.Computes100Points (5 ms)
38: [ RUN ] SurfaceAreaTest.Computes100PointsWithRectangularPBC
38: [ OK ] SurfaceAreaTest.Computes100PointsWithRectangularPBC (14 ms)
38: [ RUN ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC
38: [ OK ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC (16 ms)
38: [----------] 10 tests from SurfaceAreaTest (62 ms total)
38:
38: [----------] 4 tests from TopologyInformation
38: [ RUN ] TopologyInformation.CantWorkWithoutReadingAFile
38: [ OK ] TopologyInformation.CantWorkWithoutReadingAFile (0 ms)
38: [ RUN ] TopologyInformation.WorksWithGroFile
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] TopologyInformation.WorksWithGroFile (24 ms)
38: [ RUN ] TopologyInformation.WorksWithPdbFile
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] TopologyInformation.WorksWithPdbFile (23 ms)
38: [ RUN ] TopologyInformation.WorksWithTprFromPdbFile
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]:
38: For a correct single-point energy evaluation with nsteps = 0, use
38: continuation = yes to avoid constraining the input coordinates.
38:
38: Setting the LD random seed to 2136897967
38: Generated 330891 of the 330891 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 330891 of the 330891 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
38:
38: NOTE 2 [file lysozyme.top, line 1465]:
38: System has non-zero total charge: 2.000000
38: Total charge should normally be an integer. See
38: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
38: for discussion on how close it should be to an integer.
38:
38:
38:
38: Number of degrees of freedom in T-Coupling group rest is 465.00
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]:
38: NVE simulation with an initial temperature of zero: will use a Verlet
38: buffer of 10%. Check your energy drift!
38:
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 4 notes
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
38: Analysing residue names:
38: There are: 10 Protein residues
38: Analysing Protein...
38: This run will generate roughly 0 Mb of data
38: [ OK ] TopologyInformation.WorksWithTprFromPdbFile (3521 ms)
38: [----------] 4 tests from TopologyInformation (3568 ms total)
38:
38: [----------] 4 tests from TrajectoryModuleTest
38: [ RUN ] TrajectoryModuleTest.BasicTest
38: Reading frames from gro file 'Test system', 15 atoms.
38:
Reading frame 0 time 0.000
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38:
Reading frame 1 time 0.000
Last frame 1 time 0.000
38: Analyzed 2 frames, last time 0.000
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] TrajectoryModuleTest.BasicTest (20 ms)
38: [ RUN ] TrajectoryModuleTest.PlotsXOnly
38: Reading frames from gro file 'Test system', 15 atoms.
38:
Reading frame 0 time 0.000
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38:
Reading frame 1 time 0.000
Last frame 1 time 0.000
38: Analyzed 2 frames, last time 0.000
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] TrajectoryModuleTest.PlotsXOnly (20 ms)
38: [ RUN ] TrajectoryModuleTest.HandlesNoVelocities
38: Reading frames from gro file 'Test system', 15 atoms.
38:
Reading frame 0 time 0.000
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38:
Reading frame 1 time 0.000
Last frame 1 time 0.000
38: Analyzed 2 frames, last time 0.000
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] TrajectoryModuleTest.HandlesNoVelocities (18 ms)
38: [ RUN ] TrajectoryModuleTest.HandlesNoForces
38: Reading frames from gro file 'Test system', 15 atoms.
38:
Reading frame 0 time 0.000
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38:
Reading frame 1 time 0.000
Last frame 1 time 0.000
38: Analyzed 2 frames, last time 0.000
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] TrajectoryModuleTest.HandlesNoForces (18 ms)
38: [----------] 4 tests from TrajectoryModuleTest (77 ms total)
38:
38: [----------] 5 tests from UnionFinderTest
38: [ RUN ] UnionFinderTest.WorksEmpty
38: [ OK ] UnionFinderTest.WorksEmpty (1 ms)
38: [ RUN ] UnionFinderTest.BasicMerges
38: [ OK ] UnionFinderTest.BasicMerges (0 ms)
38: [ RUN ] UnionFinderTest.LargerMerges
38: [ OK ] UnionFinderTest.LargerMerges (0 ms)
38: [ RUN ] UnionFinderTest.LongRightMerge
38: [ OK ] UnionFinderTest.LongRightMerge (0 ms)
38: [ RUN ] UnionFinderTest.LongLeftMerge
38: [ OK ] UnionFinderTest.LongLeftMerge (0 ms)
38: [----------] 5 tests from UnionFinderTest (1 ms total)
38:
38: [----------] 1 test from MappedUnionFinderTest
38: [ RUN ] MappedUnionFinderTest.BasicMerges
38: [ OK ] MappedUnionFinderTest.BasicMerges (0 ms)
38: [----------] 1 test from MappedUnionFinderTest (0 ms total)
38:
38: [----------] Global test environment tear-down
38: [==========] 80 tests from 16 test cases ran. (6879 ms total)
38: [ PASSED ] 80 tests.
38/52 Test #38: TrajectoryAnalysisUnitTests ......... Passed 6.95 sec
test 39
Start 39: EnergyAnalysisUnitTests
39: Test command: /<<PKGBUILDDIR>>/build/basic/bin/energyanalysis-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/EnergyAnalysisUnitTests.xml"
39: Test timeout computed to be: 30
39: [==========] Running 7 tests from 4 test cases.
39: [----------] Global test environment set-up.
39: [----------] 1 test from DhdlTest
39: [ RUN ] DhdlTest.ExtractDhdl
39: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/dhdl.edr as double precision energy file
39: Reading file /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/dhdl.tpr, VERSION 2016-dev-20160810-e3ded7f (double precision)
39: Note: file tpx version 110, software tpx version 119
39:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.010
Reading energy frame 2 time 0.020
Reading energy frame 3 time 0.030
Reading energy frame 4 time 0.040
Reading energy frame 5 time 0.050
Reading energy frame 6 time 0.060
Reading energy frame 7 time 0.070
Reading energy frame 8 time 0.080
Reading energy frame 9 time 0.090
Reading energy frame 10 time 0.100
Reading energy frame 11 time 0.110
Reading energy frame 12 time 0.120
Reading energy frame 13 time 0.130
Reading energy frame 14 time 0.140
Reading energy frame 15 time 0.150
Reading energy frame 16 time 0.160
Reading energy frame 17 time 0.170
Reading energy frame 18 time 0.180
Reading energy frame 19 time 0.190
Reading energy frame 20 time 0.200
Reading energy frame 30 time 0.300
Reading energy frame 40 time 0.400
Reading energy frame 50 time 0.500
Reading energy frame 60 time 0.600
Reading energy frame 70 time 0.700
Reading energy frame 80 time 0.800
Reading energy frame 90 time 0.900
Reading energy frame 100 time 1.000
Last energy frame read 100 time 1.000
39:
39:
39: Wrote 8 lambda values with 101 samples as 808 dH data blocks to /<<PKGBUILDDIR>>/build/basic/src/gromacs/energyanalysis/tests/Testing/Temporary/DhdlTest_ExtractDhdl_dhdl.xvg
39: [ OK ] DhdlTest.ExtractDhdl (86 ms)
39: [----------] 1 test from DhdlTest (89 ms total)
39:
39: [----------] 1 test from OriresTest
39: [ RUN ] OriresTest.ExtractOrires
39: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/orires.edr as single precision energy file
39: Reading file /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/orires.tpr, VERSION 2017-dev-20170725-fea8651 (single precision)
39: Note: file tpx version 111, software tpx version 119
39: Found 7 orientation restraints with 1 experimentsSelect the orientation restraint labels you want (-1 is all)
39: End your selection with 0
39: Selecting all 7 orientation restraints
39:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.002
Reading energy frame 2 time 0.004
Reading energy frame 3 time 0.006
Reading energy frame 4 time 0.008
Reading energy frame 5 time 0.010
Reading energy frame 6 time 0.012
Reading energy frame 7 time 0.014
Reading energy frame 8 time 0.016
Reading energy frame 9 time 0.018
Reading energy frame 10 time 0.020
Last energy frame read 10 time 0.020
39: [ OK ] OriresTest.ExtractOrires (70 ms)
39: [----------] 1 test from OriresTest (71 ms total)
39:
39: [----------] 3 tests from EnergyTest
39: [ RUN ] EnergyTest.ExtractEnergy
39: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
39:
39: Select the terms you want from the following list by
39: selecting either (part of) the name or the number or a combination.
39: End your selection with an empty line or a zero.
39: -------------------------------------------------------------------
39: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip.
39: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature
39: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y
39: 13 Box-Z 14 Volume 15 Density 16 pV
39: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ
39: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX
39: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY
39: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ
39: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen
39: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System
39:
39:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
39:
39: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets
39: All statistics are over 5001 points
39:
39: Energy Average Err.Est. RMSD Tot-Drift
39: -------------------------------------------------------------------------------
39: Potential -34142.2 39 228.993 -62.8906 (kJ/mol)
39: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol)
39: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol)
39: [ OK ] EnergyTest.ExtractEnergy (23 ms)
39: [ RUN ] EnergyTest.ExtractEnergyByNumber
39: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
39:
39: Select the terms you want from the following list by
39: selecting either (part of) the name or the number or a combination.
39: End your selection with an empty line or a zero.
39: -------------------------------------------------------------------
39: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip.
39: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature
39: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y
39: 13 Box-Z 14 Volume 15 Density 16 pV
39: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ
39: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX
39: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY
39: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ
39: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen
39: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System
39:
39:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
39:
39: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets
39: All statistics are over 5001 points
39:
39: Energy Average Err.Est. RMSD Tot-Drift
39: -------------------------------------------------------------------------------
39: Coul. recip. 302.771 2.8 17.5152 12.5403 (kJ/mol)
39: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol)
39: Pres. DC -268.49 3 8.52175 13.2804 (bar)
39: [ OK ] EnergyTest.ExtractEnergyByNumber (22 ms)
39: [ RUN ] EnergyTest.ExtractEnergyMixed
39: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
39:
39: Select the terms you want from the following list by
39: selecting either (part of) the name or the number or a combination.
39: End your selection with an empty line or a zero.
39: -------------------------------------------------------------------
39: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip.
39: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature
39: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y
39: 13 Box-Z 14 Volume 15 Density 16 pV
39: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ
39: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX
39: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY
39: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ
39: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen
39: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System
39:
39:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
39:
39: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 4 data sets
39: All statistics are over 5001 points
39:
39: Energy Average Err.Est. RMSD Tot-Drift
39: -------------------------------------------------------------------------------
39: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol)
39: Pressure 5.34371 4.1 605.307 -4.88771 (bar)
39: Box-Z 2.92457 0.0054 0.0151558 0.0234974 (nm)
39: Volume 25.0162 0.14 0.386769 0.598615 (nm^3)
39: [ OK ] EnergyTest.ExtractEnergyMixed (23 ms)
39: [----------] 3 tests from EnergyTest (71 ms total)
39:
39: [----------] 2 tests from ViscosityTest
39: [ RUN ] ViscosityTest.EinsteinViscosity
39: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
39:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
39:
39: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets
39: All statistics are over 5001 points
39:
39: Energy Average Err.Est. RMSD Tot-Drift
39: -------------------------------------------------------------------------------
39: Pres-XX 20.2092 65 717.193 185.978 (bar)
39: Pres-XY -47.7351 39 372.522 207.456 (bar)
39: Pres-XZ 11.477 31 379.79 6.80818 (bar)
39: Pres-YX -47.7106 39 372.525 207.5 (bar)
39: Pres-YY 38.9241 40 803.899 -27.1505 (bar)
39: Pres-YZ -41.3534 45 401.216 114.663 (bar)
39: Pres-ZX 11.5238 31 379.804 6.91707 (bar)
39: Pres-ZY -41.3119 45 401.196 114.743 (bar)
39: Pres-ZZ -43.1021 63 748.522 -173.491 (bar)
39: Temperature 300.001 0.02 5.8425 -0.0130558 (K)
39: Volume 25.0162 0.14 0.386769 0.598615 (nm^3)
39: Pressure 5.34371 4.1 605.307 -4.88771 (bar)
39: [ OK ] ViscosityTest.EinsteinViscosity (46 ms)
39: [ RUN ] ViscosityTest.EinsteinViscosityIntegral
39: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
39:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
39:
39: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets
39: All statistics are over 5001 points
39:
39: Energy Average Err.Est. RMSD Tot-Drift
39: -------------------------------------------------------------------------------
39: Pres-XX 20.2092 65 717.193 185.978 (bar)
39: Pres-XY -47.7351 39 372.522 207.456 (bar)
39: Pres-XZ 11.477 31 379.79 6.80818 (bar)
39: Pres-YX -47.7106 39 372.525 207.5 (bar)
39: Pres-YY 38.9241 40 803.899 -27.1505 (bar)
39: Pres-YZ -41.3534 45 401.216 114.663 (bar)
39: Pres-ZX 11.5238 31 379.804 6.91707 (bar)
39: Pres-ZY -41.3119 45 401.196 114.743 (bar)
39: Pres-ZZ -43.1021 63 748.522 -173.491 (bar)
39: Temperature 300.001 0.02 5.8425 -0.0130558 (K)
39: Volume 25.0162 0.14 0.386769 0.598615 (nm^3)
39: Pressure 5.34371 4.1 605.307 -4.88771 (bar)
39: [ OK ] ViscosityTest.EinsteinViscosityIntegral (40 ms)
39: [----------] 2 tests from ViscosityTest (88 ms total)
39:
39: [----------] Global test environment tear-down
39: [==========] 7 tests from 4 test cases ran. (322 ms total)
39: [ PASSED ] 7 tests.
39/52 Test #39: EnergyAnalysisUnitTests ............. Passed 0.39 sec
test 40
Start 40: ToolUnitTests
40: Test command: /<<PKGBUILDDIR>>/build/basic/bin/tool-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/ToolUnitTests.xml"
40: Test timeout computed to be: 30
40: [==========] Running 18 tests from 4 test cases.
40: [----------] Global test environment set-up.
40: [----------] 2 tests from DumpTest
40:
40: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]:
40: For a correct single-point energy evaluation with nsteps = 0, use
40: continuation = yes to avoid constraining the input coordinates.
40:
40: Setting the LD random seed to -2082070198
40: Generated 330891 of the 330891 non-bonded parameter combinations
40: Generating 1-4 interactions: fudge = 0.5
40: Generated 330891 of the 330891 1-4 parameter combinations
40: Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
40:
40: NOTE 2 [file lysozyme.top, line 1465]:
40: System has non-zero total charge: 2.000000
40: Total charge should normally be an integer. See
40: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
40: for discussion on how close it should be to an integer.
40:
40:
40:
40: Number of degrees of freedom in T-Coupling group rest is 465.00
40:
40: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]:
40: NVE simulation with an initial temperature of zero: will use a Verlet
40: buffer of 10%. Check your energy drift!
40:
40:
40: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]:
40: You are using a plain Coulomb cut-off, which might produce artifacts.
40: You might want to consider using PME electrostatics.
40:
40:
40:
40: There were 4 notes
40: Analysing residue names:
40: There are: 10 Protein residues
40: Analysing Protein...
40: This run will generate roughly 0 Mb of data
40: [ RUN ] DumpTest.WorksWithTpr
40: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
40: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
40: /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr:
40: inputrec:
40: integrator = md
40: tinit = 0
40: dt = 0.001
40: nsteps = 0
40: init-step = 0
40: simulation-part = 1
40: comm-mode = Linear
40: nstcomm = 100
40: bd-fric = 0
40: ld-seed = -2082070198
40: emtol = 10
40: emstep = 0.01
40: niter = 20
40: fcstep = 0
40: nstcgsteep = 1000
40: nbfgscorr = 10
40: rtpi = 0.05
40: nstxout = 0
40: nstvout = 0
40: nstfout = 0
40: nstlog = 1000
40: nstcalcenergy = 100
40: nstenergy = 1000
40: nstxout-compressed = 0
40: compressed-x-precision = 1000
40: cutoff-scheme = Verlet
40: nstlist = 10
40: pbc = xyz
40: periodic-molecules = false
40: verlet-buffer-tolerance = -1
40: rlist = 1.1
40: coulombtype = Cut-off
40: coulomb-modifier = Potential-shift
40: rcoulomb-switch = 0
40: rcoulomb = 1
40: epsilon-r = 1
40: epsilon-rf = inf
40: vdw-type = Cut-off
40: vdw-modifier = Potential-shift
40: rvdw-switch = 0
40: rvdw = 1
40: DispCorr = No
40: table-extension = 1
40: fourierspacing = 0.12
40: fourier-nx = 0
40: fourier-ny = 0
40: fourier-nz = 0
40: pme-order = 4
40: ewald-rtol = 1e-05
40: ewald-rtol-lj = 0.001
40: lj-pme-comb-rule = Geometric
40: ewald-geometry = 0
40: epsilon-surface = 0
40: tcoupl = No
40: nsttcouple = -1
40: nh-chain-length = 0
40: print-nose-hoover-chain-variables = false
40: pcoupl = No
40: pcoupltype = Isotropic
40: nstpcouple = -1
40: tau-p = 1
40: compressibility (3x3):
40: compressibility[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: compressibility[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: compressibility[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: ref-p (3x3):
40: ref-p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: ref-p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: refcoord-scaling = No
40: posres-com (3):
40: posres-com[0]= 0.00000e+00
40: posres-com[1]= 0.00000e+00
40: posres-com[2]= 0.00000e+00
40: posres-comB (3):
40: posres-comB[0]= 0.00000e+00
40: posres-comB[1]= 0.00000e+00
40: posres-comB[2]= 0.00000e+00
40: QMMM = false
40: QMconstraints = 0
40: QMMMscheme = 0
40: MMChargeScaleFactor = 1
40: qm-opts:
40: ngQM = 0
40: constraint-algorithm = Lincs
40: continuation = false
40: Shake-SOR = false
40: shake-tol = 0.0001
40: lincs-order = 4
40: lincs-iter = 1
40: lincs-warnangle = 30
40: nwall = 0
40: wall-type = 9-3
40: wall-r-linpot = -1
40: wall-atomtype[0] = -1
40: wall-atomtype[1] = -1
40: wall-density[0] = 0
40: wall-density[1] = 0
40: wall-ewald-zfac = 3
40: pull = false
40: awh = false
40: rotation = false
40: interactiveMD = false
40: disre = No
40: disre-weighting = Conservative
40: disre-mixed = false
40: dr-fc = 1000
40: dr-tau = 0
40: nstdisreout = 100
40: orire-fc = 0
40: orire-tau = 0
40: nstorireout = 100
40: free-energy = no
40: cos-acceleration = 0
40: deform (3x3):
40: deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: simulated-tempering = false
40: swapcoords = no
40: userint1 = 0
40: userint2 = 0
40: userint3 = 0
40: userint4 = 0
40: userreal1 = 0
40: userreal2 = 0
40: userreal3 = 0
40: userreal4 = 0
40: applied-forces:
40: electric-field:
40: x:
40: E0 = 0
40: omega = 0
40: t0 = 0
40: sigma = 0
40: y:
40: E0 = 0
40: omega = 0
40: t0 = 0
40: sigma = 0
40: z:
40: E0 = 0
40: omega = 0
40: t0 = 0
40: sigma = 0
40: density-guided-simulation:
40: active = false
40: group = protein
40: similarity-measure = inner-product
40: atom-spreading-weight = unity
40: force-constant = 1e+09
40: gaussian-transform-spreading-width = 0.2
40: gaussian-transform-spreading-range-in-multiples-of-width = 4
40: reference-density-filename = reference.mrc
40: nst = 1
40: normalize-densities = true
40: adaptive-force-scaling = false
40: adaptive-force-scaling-time-constant = 4
40: grpopts:
40: nrdf: 465
40: ref-t: 0
40: tau-t: 0
40: annealing: No
40: annealing-npoints: 0
40: acc: 0 0 0
40: nfreeze: N N N
40: energygrp-flags[ 0]: 0
40: header:
40: bIr = present
40: bBox = present
40: bTop = present
40: bX = present
40: bV = present
40: bF = not present
40: natoms = 156
40: lambda = 0.000000e+00
40: buffer size = 59422
40: topology:
40: name="First 10 residues from 1AKI"
40: #atoms = 156
40: #molblock = 1
40: molblock (0):
40: moltype = 0 "Protein_chain_B"
40: #molecules = 1
40: #posres_xA = 0
40: #posres_xB = 0
40: bIntermolecularInteractions = false
40: ffparams:
40: atnr=10
40: ntypes=212
40: functype[0]=LJ_SR, c6= 3.35274590e-03, c12= 3.95094276e-06
40: functype[1]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
40: functype[2]=LJ_SR, c6= 2.60916958e-03, c12= 3.84022405e-06
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40: functype[46]=LJ_SR, c6= 3.38512054e-03, c12= 7.98643487e-06
40: functype[47]=LJ_SR, c6= 7.02015939e-04, c12= 5.24670895e-07
40: functype[48]=LJ_SR, c6= 7.28404266e-04, c12= 4.37535846e-07
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40: functype[52]=LJ_SR, c6= 2.19085021e-03, c12= 2.43608270e-06
40: functype[53]=LJ_SR, c6= 5.38290828e-04, c12= 2.18128321e-07
40: functype[54]=LJ_SR, c6= 3.39879468e-03, c12= 4.64829736e-06
40: functype[55]=LJ_SR, c6= 2.36385735e-03, c12= 1.58990645e-06
40: functype[56]=LJ_SR, c6= 2.35434738e-03, c12= 2.73168575e-06
40: functype[57]=LJ_SR, c6= 4.88250953e-04, c12= 1.79458596e-07
40: functype[58]=LJ_SR, c6= 5.06604381e-04, c12= 1.49655136e-07
40: functype[59]=LJ_SR, c6= 6.04976481e-03, c12= 7.32016997e-06
40: functype[60]=LJ_SR, c6= 2.80388421e-03, c12= 4.30620821e-06
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40: functype[62]=LJ_SR, c6= 2.18203571e-03, c12= 4.18553600e-06
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40: functype[64]=LJ_SR, c6= 3.38512054e-03, c12= 7.98643487e-06
40: functype[65]=LJ_SR, c6= 2.35434738e-03, c12= 2.73168575e-06
40: functype[66]=LJ_SR, c6= 2.34487536e-03, c12= 4.69342376e-06
40: functype[67]=LJ_SR, c6= 4.86286852e-04, c12= 3.08335643e-07
40: functype[68]=LJ_SR, c6= 5.04566357e-04, c12= 2.57128875e-07
40: functype[69]=LJ_SR, c6= 6.02542516e-03, c12= 1.25770912e-05
40: functype[70]=LJ_SR, c6= 5.81477652e-04, c12= 2.82897616e-07
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40: functype[72]=LJ_SR, c6= 4.52516542e-04, c12= 2.74969580e-07
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40: functype[74]=LJ_SR, c6= 7.02015939e-04, c12= 5.24670895e-07
40: functype[75]=LJ_SR, c6= 4.88250953e-04, c12= 1.79458596e-07
40: functype[76]=LJ_SR, c6= 4.86286852e-04, c12= 3.08335643e-07
40: functype[77]=LJ_SR, c6= 1.00847494e-04, c12= 2.02561683e-08
40: functype[78]=LJ_SR, c6= 1.04638377e-04, c12= 1.68921392e-08
40: functype[79]=LJ_SR, c6= 1.24956947e-03, c12= 8.26254961e-07
40: functype[80]=LJ_SR, c6= 6.03335386e-04, c12= 2.35915493e-07
40: functype[81]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
40: functype[82]=LJ_SR, c6= 4.69526683e-04, c12= 2.29304163e-07
40: functype[83]=LJ_SR, c6= 1.15362534e-04, c12= 2.05320472e-08
40: functype[84]=LJ_SR, c6= 7.28404266e-04, c12= 4.37535846e-07
40: functype[85]=LJ_SR, c6= 5.06604381e-04, c12= 1.49655136e-07
40: functype[86]=LJ_SR, c6= 5.04566357e-04, c12= 2.57128875e-07
40: functype[87]=LJ_SR, c6= 1.04638377e-04, c12= 1.68921392e-08
40: functype[88]=LJ_SR, c6= 1.08571716e-04, c12= 1.40867806e-08
40: functype[89]=LJ_SR, c6= 1.29654107e-03, c12= 6.89035176e-07
40: functype[90]=LJ_SR, c6= 7.20490469e-03, c12= 1.15394714e-05
40: functype[91]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
40: functype[92]=LJ_SR, c6= 5.60698984e-03, c12= 1.12160897e-05
40: functype[93]=LJ_SR, c6= 1.37763575e-03, c12= 1.00429668e-06
40: functype[94]=LJ_SR, c6= 8.69845692e-03, c12= 2.14014708e-05
40: functype[95]=LJ_SR, c6= 6.04976481e-03, c12= 7.32016997e-06
40: functype[96]=LJ_SR, c6= 6.02542516e-03, c12= 1.25770912e-05
40: functype[97]=LJ_SR, c6= 1.24956947e-03, c12= 8.26254961e-07
40: functype[98]=LJ_SR, c6= 1.29654107e-03, c12= 6.89035176e-07
40: functype[99]=LJ_SR, c6= 1.54830217e-02, c12= 3.37031743e-05
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40: functype[101]=BONDS, b0A= 1.47100e-01, cbA= 3.07106e+05, b0B= 1.47100e-01, cbB= 3.07106e+05
40: functype[102]=BONDS, b0A= 1.09000e-01, cbA= 2.84512e+05, b0B= 1.09000e-01, cbB= 2.84512e+05
40: functype[103]=BONDS, b0A= 1.52900e-01, cbA= 2.24262e+05, b0B= 1.52900e-01, cbB= 2.24262e+05
40: functype[104]=BONDS, b0A= 1.52200e-01, cbA= 2.65266e+05, b0B= 1.52200e-01, cbB= 2.65266e+05
40: functype[105]=BONDS, b0A= 1.22900e-01, cbA= 4.76976e+05, b0B= 1.22900e-01, cbB= 4.76976e+05
40: functype[106]=BONDS, b0A= 1.33500e-01, cbA= 4.10032e+05, b0B= 1.33500e-01, cbB= 4.10032e+05
40: functype[107]=BONDS, b0A= 1.44900e-01, cbA= 2.82002e+05, b0B= 1.44900e-01, cbB= 2.82002e+05
40: functype[108]=BONDS, b0A= 1.51000e-01, cbA= 2.65266e+05, b0B= 1.51000e-01, cbB= 2.65266e+05
40: functype[109]=BONDS, b0A= 1.40000e-01, cbA= 3.92459e+05, b0B= 1.40000e-01, cbB= 3.92459e+05
40: functype[110]=BONDS, b0A= 1.08000e-01, cbA= 3.07106e+05, b0B= 1.08000e-01, cbB= 3.07106e+05
40: functype[111]=BONDS, b0A= 1.46300e-01, cbA= 2.82002e+05, b0B= 1.46300e-01, cbB= 2.82002e+05
40: functype[112]=BONDS, b0A= 1.34000e-01, cbA= 4.02501e+05, b0B= 1.34000e-01, cbB= 4.02501e+05
40: functype[113]=BONDS, b0A= 1.81000e-01, cbA= 1.85770e+05, b0B= 1.81000e-01, cbB= 1.85770e+05
40: functype[114]=BONDS, b0A= 1.33600e-01, cbA= 2.29283e+05, b0B= 1.33600e-01, cbB= 2.29283e+05
40: functype[115]=BONDS, b0A= 1.25000e-01, cbA= 5.48941e+05, b0B= 1.25000e-01, cbB= 5.48941e+05
40: functype[116]=ANGLES, thA= 1.09500e+02, ctA= 2.92880e+02, thB= 1.09500e+02, ctB= 2.92880e+02
40: functype[117]=ANGLES, thA= 1.11200e+02, ctA= 6.69440e+02, thB= 1.11200e+02, ctB= 6.69440e+02
40: functype[118]=ANGLES, thA= 1.10700e+02, ctA= 3.13800e+02, thB= 1.10700e+02, ctB= 3.13800e+02
40: functype[119]=ANGLES, thA= 1.11100e+02, ctA= 5.27184e+02, thB= 1.11100e+02, ctB= 5.27184e+02
40: functype[120]=ANGLES, thA= 1.12700e+02, ctA= 4.88273e+02, thB= 1.12700e+02, ctB= 4.88273e+02
40: functype[121]=ANGLES, thA= 1.07800e+02, ctA= 2.76144e+02, thB= 1.07800e+02, ctB= 2.76144e+02
40: functype[122]=ANGLES, thA= 1.20400e+02, ctA= 6.69440e+02, thB= 1.20400e+02, ctB= 6.69440e+02
40: functype[123]=ANGLES, thA= 1.16600e+02, ctA= 5.85760e+02, thB= 1.16600e+02, ctB= 5.85760e+02
40: functype[124]=ANGLES, thA= 1.22900e+02, ctA= 6.69440e+02, thB= 1.22900e+02, ctB= 6.69440e+02
40: functype[125]=ANGLES, thA= 1.19800e+02, ctA= 2.92880e+02, thB= 1.19800e+02, ctB= 2.92880e+02
40: functype[126]=ANGLES, thA= 1.21900e+02, ctA= 4.18400e+02, thB= 1.21900e+02, ctB= 4.18400e+02
40: functype[127]=ANGLES, thA= 1.18400e+02, ctA= 3.17984e+02, thB= 1.18400e+02, ctB= 3.17984e+02
40: functype[128]=ANGLES, thA= 1.09700e+02, ctA= 6.69440e+02, thB= 1.09700e+02, ctB= 6.69440e+02
40: functype[129]=ANGLES, thA= 1.10100e+02, ctA= 5.27184e+02, thB= 1.10100e+02, ctB= 5.27184e+02
40: functype[130]=ANGLES, thA= 1.14000e+02, ctA= 5.27184e+02, thB= 1.14000e+02, ctB= 5.27184e+02
40: functype[131]=ANGLES, thA= 1.20000e+02, ctA= 5.85760e+02, thB= 1.20000e+02, ctB= 5.85760e+02
40: functype[132]=ANGLES, thA= 1.20000e+02, ctA= 5.27184e+02, thB= 1.20000e+02, ctB= 5.27184e+02
40: functype[133]=ANGLES, thA= 1.20000e+02, ctA= 2.92880e+02, thB= 1.20000e+02, ctB= 2.92880e+02
40: functype[134]=ANGLES, thA= 1.18400e+02, ctA= 2.92880e+02, thB= 1.18400e+02, ctB= 2.92880e+02
40: functype[135]=ANGLES, thA= 1.23200e+02, ctA= 4.18400e+02, thB= 1.23200e+02, ctB= 4.18400e+02
40: functype[136]=ANGLES, thA= 1.08600e+02, ctA= 4.18400e+02, thB= 1.08600e+02, ctB= 4.18400e+02
40: functype[137]=ANGLES, thA= 9.60000e+01, ctA= 3.68192e+02, thB= 9.60000e+01, ctB= 3.68192e+02
40: functype[138]=ANGLES, thA= 1.17000e+02, ctA= 5.85760e+02, thB= 1.17000e+02, ctB= 5.85760e+02
40: functype[139]=ANGLES, thA= 1.26000e+02, ctA= 6.69440e+02, thB= 1.26000e+02, ctB= 6.69440e+02
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40: functype[141]=PDIHS, phiA= 1.80000000e+02, cpA= 4.18400002e+00, phiB= 1.80000000e+02, cpB= 4.18400002e+00, mult=2
40: functype[142]=PDIHS, phiA= 1.80000000e+02, cpA= 4.60239983e+00, phiB= 1.80000000e+02, cpB= 4.60239983e+00, mult=2
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40: rbcB[0]= 2.92880011e+00, rbcB[1]=-1.46440005e+00, rbcB[2]= 2.09199995e-01, rbcB[3]=-1.67359996e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[153]=RBDIHS, rbcA[0]= 5.77183008e+00, rbcA[1]=-2.67147994e+00, rbcA[2]= 9.58140016e-01, rbcA[3]=-4.05847979e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 5.77183008e+00, rbcB[1]=-2.67147994e+00, rbcB[2]= 9.58140016e-01, rbcB[3]=-4.05847979e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[154]=RBDIHS, rbcA[0]= 8.03330004e-01, rbcA[1]= 2.40999007e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.21331000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 8.03330004e-01, rbcB[1]= 2.40999007e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.21331000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[155]=RBDIHS, rbcA[0]= 2.05016003e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.05016003e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 2.05016003e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.05016003e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[156]=RBDIHS, rbcA[0]= 3.02879791e+01, rbcA[1]=-4.81160021e+00, rbcA[2]=-2.54763794e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 3.02879791e+01, rbcB[1]=-4.81160021e+00, rbcB[2]=-2.54763794e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[157]=RBDIHS, rbcA[0]= 2.54763794e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.54763794e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 2.54763794e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.54763794e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[158]=RBDIHS, rbcA[0]= 1.57025499e+01, rbcA[1]= 3.17565594e+01, rbcA[2]=-3.66935992e+00, rbcA[3]=-4.37897491e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 1.57025499e+01, rbcB[1]= 3.17565594e+01, rbcB[2]=-3.66935992e+00, rbcB[3]=-4.37897491e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[159]=RBDIHS, rbcA[0]=-1.03574896e+01, rbcA[1]=-2.95871601e+01, rbcA[2]=-1.16734004e+00, rbcA[3]= 4.11119919e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]=-1.03574896e+01, rbcB[1]=-2.95871601e+01, rbcB[2]=-1.16734004e+00, rbcB[3]= 4.11119919e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[160]=RBDIHS, rbcA[0]= 4.50198984e+00, rbcA[1]= 7.82410026e-01, rbcA[2]=-1.60247004e+00, rbcA[3]=-3.68192005e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 4.50198984e+00, rbcB[1]= 7.82410026e-01, rbcB[2]=-1.60247004e+00, rbcB[3]=-3.68192005e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[161]=RBDIHS, rbcA[0]= 4.22589988e-01, rbcA[1]= 2.70705009e+00, rbcA[2]=-3.12964010e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 4.22589988e-01, rbcB[1]= 2.70705009e+00, rbcB[2]=-3.12964010e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[162]=RBDIHS, rbcA[0]=-7.65670002e-01, rbcA[1]= 2.70705009e+00, rbcA[2]= 4.02501011e+00, rbcA[3]=-5.96639013e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]=-7.65670002e-01, rbcB[1]= 2.70705009e+00, rbcB[2]= 4.02501011e+00, rbcB[3]=-5.96639013e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[163]=RBDIHS, rbcA[0]= 9.66499984e-01, rbcA[1]= 2.89950991e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.86600995e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 9.66499984e-01, rbcB[1]= 2.89950991e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.86600995e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[164]=RBDIHS, rbcA[0]=-4.23421001e+00, rbcA[1]= 7.22159004e+00, rbcA[2]= 1.90789998e+00, rbcA[3]=-4.89527988e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]=-4.23421001e+00, rbcB[1]= 7.22159004e+00, rbcB[2]= 1.90789998e+00, rbcB[3]=-4.89527988e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[165]=RBDIHS, rbcA[0]= 3.03339996e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.03339996e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 3.03339996e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.03339996e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[166]=RBDIHS, rbcA[0]= 1.02319698e+01, rbcA[1]= 3.52082992e+00, rbcA[2]=-3.97899008e+00, rbcA[3]=-9.77381992e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 1.02319698e+01, rbcB[1]= 3.52082992e+00, rbcB[2]=-3.97899008e+00, rbcB[3]=-9.77381992e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[167]=RBDIHS, rbcA[0]= 5.49777985e+00, rbcA[1]= 1.41838002e+00, rbcA[2]=-6.91615009e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 5.49777985e+00, rbcB[1]= 1.41838002e+00, rbcB[2]=-6.91615009e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[168]=RBDIHS, rbcA[0]=-1.21755004e+00, rbcA[1]=-3.65264010e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 4.87018013e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]=-1.21755004e+00, rbcB[1]=-3.65264010e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 4.87018013e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[169]=RBDIHS, rbcA[0]=-1.26775002e+00, rbcA[1]= 3.02084994e+00, rbcA[2]= 1.74473000e+00, rbcA[3]=-3.49781990e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]=-1.26775002e+00, rbcB[1]= 3.02084994e+00, rbcB[2]= 1.74473000e+00, rbcB[3]=-3.49781990e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[170]=RBDIHS, rbcA[0]= 3.80117011e+00, rbcA[1]=-6.95172024e+00, rbcA[2]=-1.01671004e+00, rbcA[3]= 4.16726017e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 3.80117011e+00, rbcB[1]=-6.95172024e+00, rbcB[2]=-1.01671004e+00, rbcB[3]= 4.16726017e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[171]=RBDIHS, rbcA[0]= 3.70279998e-01, rbcA[1]= 1.11085999e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-1.48114002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 3.70279998e-01, rbcB[1]= 1.11085999e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-1.48114002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[172]=RBDIHS, rbcA[0]= 3.32042198e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.32042198e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 3.32042198e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.32042198e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[173]=RBDIHS, rbcA[0]= 1.63176003e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-1.63176003e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 1.63176003e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-1.63176003e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[174]=RBDIHS, rbcA[0]= 3.40787005e+00, rbcA[1]=-2.80537009e+00, rbcA[2]=-3.59820008e-01, rbcA[3]=-2.42670000e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 3.40787005e+00, rbcB[1]=-2.80537009e+00, rbcB[2]=-3.59820008e-01, rbcB[3]=-2.42670000e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[175]=RBDIHS, rbcA[0]=-1.62590199e+01, rbcA[1]= 9.08765030e+00, rbcA[2]= 7.17138004e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]=-1.62590199e+01, rbcB[1]= 9.08765030e+00, rbcB[2]= 7.17138004e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[176]=RBDIHS, rbcA[0]= 9.45590019e-01, rbcA[1]= 2.83675003e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.78234005e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 9.45590019e-01, rbcB[1]= 2.83675003e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.78234005e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[177]=RBDIHS, rbcA[0]=-1.50624001e+00, rbcA[1]= 5.37225008e+00, rbcA[2]= 1.17989004e+00, rbcA[3]=-5.04589987e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]=-1.50624001e+00, rbcB[1]= 5.37225008e+00, rbcB[2]= 1.17989004e+00, rbcB[3]=-5.04589987e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[178]=RBDIHS, rbcA[0]= 1.00416005e+00, rbcA[1]= 3.01248002e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-4.01664019e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 1.00416005e+00, rbcB[1]= 3.01248002e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-4.01664019e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[179]=RBDIHS, rbcA[0]= 8.79267979e+00, rbcA[1]=-1.18344402e+01, rbcA[2]= 1.07528996e+00, rbcA[3]= 1.96648002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 8.79267979e+00, rbcB[1]=-1.18344402e+01, rbcB[2]= 1.07528996e+00, rbcB[3]= 1.96648002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[180]=RBDIHS, rbcA[0]=-5.77392006e+00, rbcA[1]= 3.38485003e+00, rbcA[2]= 2.38906002e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]=-5.77392006e+00, rbcB[1]= 3.38485003e+00, rbcB[2]= 2.38906002e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[181]=RBDIHS, rbcA[0]=-9.08345985e+00, rbcA[1]= 9.75708961e+00, rbcA[2]= 3.45180011e+00, rbcA[3]=-4.12542009e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]=-9.08345985e+00, rbcB[1]= 9.75708961e+00, rbcB[2]= 3.45180011e+00, rbcB[3]=-4.12542009e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[182]=RBDIHS, rbcA[0]=-4.70699996e-01, rbcA[1]=-1.41209996e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 1.88279998e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]=-4.70699996e-01, rbcB[1]=-1.41209996e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 1.88279998e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[183]=RBDIHS, rbcA[0]= 3.43088007e+00, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.43088007e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 3.43088007e+00, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.43088007e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[184]=RBDIHS, rbcA[0]= 2.57315993e+00, rbcA[1]= 3.49781990e+00, rbcA[2]=-1.10038996e+00, rbcA[3]=-4.97059011e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 2.57315993e+00, rbcB[1]= 3.49781990e+00, rbcB[2]=-1.10038996e+00, rbcB[3]=-4.97059011e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[185]=RBDIHS, rbcA[0]=-8.22160006e-01, rbcA[1]= 1.12758994e+00, rbcA[2]=-3.05440009e-01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]=-8.22160006e-01, rbcB[1]= 1.12758994e+00, rbcB[2]=-3.05440009e-01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[186]=LJ14, c6A= 3.20536114e-04, c12A= 1.71928207e-07, c6B= 3.20536114e-04, c12B= 1.71928207e-07
40: functype[187]=LJ14, c6A= 1.30458479e-03, c12A= 1.92011203e-06, c6B= 1.30458479e-03, c12B= 1.92011203e-06
40: functype[188]=LJ14, c6A= 1.40760513e-03, c12A= 1.25315830e-06, c6B= 1.40760513e-03, c12B= 1.25315830e-06
40: functype[189]=LJ14, c6A= 1.67637295e-03, c12A= 1.97547138e-06, c6B= 1.67637295e-03, c12B= 1.97547138e-06
40: functype[190]=LJ14, c6A= 0.00000000e+00, c12A= 0.00000000e+00, c6B= 0.00000000e+00, c12B= 0.00000000e+00
40: functype[191]=LJ14, c6A= 2.49447097e-04, c12A= 1.67110088e-07, c6B= 2.49447097e-04, c12B= 1.67110088e-07
40: functype[192]=LJ14, c6A= 1.01525197e-03, c12A= 1.86630257e-06, c6B= 1.01525197e-03, c12B= 1.86630257e-06
40: functype[193]=LJ14, c6A= 6.12890653e-05, c12A= 1.49631507e-08, c6B= 6.12890653e-05, c12B= 1.49631507e-08
40: functype[194]=LJ14, c6A= 2.69145414e-04, c12A= 1.09064160e-07, c6B= 2.69145414e-04, c12B= 1.09064160e-07
40: functype[195]=LJ14, c6A= 1.09542510e-03, c12A= 1.21804135e-06, c6B= 1.09542510e-03, c12B= 1.21804135e-06
40: functype[196]=LJ14, c6A= 3.86982108e-04, c12A= 3.18863499e-07, c6B= 3.86982108e-04, c12B= 3.18863499e-07
40: functype[197]=LJ14, c6A= 1.57502061e-03, c12A= 3.56110013e-06, c6B= 1.57502061e-03, c12B= 3.56110013e-06
40: functype[198]=LJ14, c6A= 2.44342256e-03, c12A= 6.79494860e-06, c6B= 2.44342256e-03, c12B= 6.79494860e-06
40: functype[199]=LJ14, c6A= 1.40194211e-03, c12A= 2.15310411e-06, c6B= 1.40194211e-03, c12B= 2.15310411e-06
40: functype[200]=LJ14, c6A= 1.09101785e-03, c12A= 2.09276800e-06, c6B= 1.09101785e-03, c12B= 2.09276800e-06
40: functype[201]=LJ14, c6A= 2.68062693e-04, c12A= 1.87387855e-07, c6B= 2.68062693e-04, c12B= 1.87387855e-07
40: functype[202]=LJ14, c6A= 2.26258271e-04, c12A= 1.37484790e-07, c6B= 2.26258271e-04, c12B= 1.37484790e-07
40: functype[203]=LJ14, c6A= 2.43143426e-04, c12A= 1.54167822e-07, c6B= 2.43143426e-04, c12B= 1.54167822e-07
40: functype[204]=LJ14, c6A= 1.17243768e-03, c12A= 2.34671188e-06, c6B= 1.17243768e-03, c12B= 2.34671188e-06
40: functype[205]=LJ14, c6A= 1.69256027e-03, c12A= 3.99321743e-06, c6B= 1.69256027e-03, c12B= 3.99321743e-06
40: functype[206]=LJ14, c6A= 5.04237469e-05, c12A= 1.01280841e-08, c6B= 5.04237469e-05, c12B= 1.01280841e-08
40: functype[207]=LJ14, c6A= 2.34763342e-04, c12A= 1.14652082e-07, c6B= 2.34763342e-04, c12B= 1.14652082e-07
40: functype[208]=LJ14, c6A= 5.76812672e-05, c12A= 1.02660236e-08, c6B= 5.76812672e-05, c12B= 1.02660236e-08
40: functype[209]=LJ14, c6A= 3.60245234e-03, c12A= 5.76973571e-06, c6B= 3.60245234e-03, c12B= 5.76973571e-06
40: functype[210]=LJ14, c6A= 6.88817876e-04, c12A= 5.02148339e-07, c6B= 6.88817876e-04, c12B= 5.02148339e-07
40: functype[211]=LJ14, c6A= 4.34922846e-03, c12A= 1.07007354e-05, c6B= 4.34922846e-03, c12B= 1.07007354e-05
40: reppow = 12
40: fudgeQQ = 0.5
40: cmap
40: atomtypes:
40: atomtype[ 0]={atomnumber= 7}
40: atomtype[ 1]={atomnumber= 1}
40: atomtype[ 2]={atomnumber= 6}
40: atomtype[ 3]={atomnumber= 1}
40: atomtype[ 4]={atomnumber= 6}
40: atomtype[ 5]={atomnumber= 8}
40: atomtype[ 6]={atomnumber= 6}
40: atomtype[ 7]={atomnumber= 1}
40: atomtype[ 8]={atomnumber= 6}
40: atomtype[ 9]={atomnumber= 16}
40: moltype (0):
40: name="Protein_chain_B"
40: atoms:
40: atom (156):
40: atom[ 0]={type= 0, typeB= 0, ptype= Atom, m= 1.40027e+01, q=-3.00000e-01, mB= 1.40027e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7}
40: atom[ 1]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
40: atom[ 2]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
40: atom[ 3]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
40: atom[ 4]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 2.50000e-01, mB= 1.20110e+01, qB= 2.50000e-01, resind= 0, atomnumber= 6}
40: atom[ 5]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
40: atom[ 6]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6}
40: atom[ 7]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
40: atom[ 8]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
40: atom[ 9]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6}
40: atom[ 10]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
40: atom[ 11]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
40: atom[ 12]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6}
40: atom[ 13]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
40: atom[ 14]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
40: atom[ 15]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 0, atomnumber= 6}
40: atom[ 16]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
40: atom[ 17]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
40: atom[ 18]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-3.00000e-01, mB= 1.40067e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7}
40: atom[ 19]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
40: atom[ 20]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
40: atom[ 21]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
40: atom[ 22]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 0, atomnumber= 6}
40: atom[ 23]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 0, atomnumber= 8}
40: atom[ 24]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 1, atomnumber= 7}
40: atom[ 25]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 1, atomnumber= 1}
40: atom[ 26]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 1, atomnumber= 6}
40: atom[ 27]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
40: atom[ 28]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 1, atomnumber= 6}
40: atom[ 29]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
40: atom[ 30]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6}
40: atom[ 31]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
40: atom[ 32]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
40: atom[ 33]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
40: atom[ 34]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6}
40: atom[ 35]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
40: atom[ 36]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
40: atom[ 37]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
40: atom[ 38]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 1, atomnumber= 6}
40: atom[ 39]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 1, atomnumber= 8}
40: atom[ 40]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 2, atomnumber= 7}
40: atom[ 41]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 2, atomnumber= 1}
40: atom[ 42]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 2, atomnumber= 6}
40: atom[ 43]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1}
40: atom[ 44]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-03, mB= 1.20110e+01, qB=-5.00000e-03, resind= 2, atomnumber= 6}
40: atom[ 45]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1}
40: atom[ 46]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1}
40: atom[ 47]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
40: atom[ 48]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
40: atom[ 49]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1}
40: atom[ 50]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
40: atom[ 51]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1}
40: atom[ 52]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
40: atom[ 53]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1}
40: atom[ 54]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
40: atom[ 55]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1}
40: atom[ 56]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
40: atom[ 57]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1}
40: atom[ 58]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 2, atomnumber= 6}
40: atom[ 59]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 2, atomnumber= 8}
40: atom[ 60]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 3, atomnumber= 7}
40: atom[ 61]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 3, atomnumber= 1}
40: atom[ 62]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 8.00000e-02, mB= 1.20110e+01, qB= 8.00000e-02, resind= 3, atomnumber= 6}
40: atom[ 63]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1}
40: atom[ 64]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1}
40: atom[ 65]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 3, atomnumber= 6}
40: atom[ 66]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 3, atomnumber= 8}
40: atom[ 67]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 4, atomnumber= 7}
40: atom[ 68]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 4, atomnumber= 1}
40: atom[ 69]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 4, atomnumber= 6}
40: atom[ 70]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
40: atom[ 71]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 4, atomnumber= 6}
40: atom[ 72]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
40: atom[ 73]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
40: atom[ 74]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-02, mB= 1.20110e+01, qB=-5.00000e-02, resind= 4, atomnumber= 6}
40: atom[ 75]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
40: atom[ 76]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
40: atom[ 77]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 4, atomnumber= 6}
40: atom[ 78]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
40: atom[ 79]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
40: atom[ 80]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-7.00000e-01, mB= 1.40067e+01, qB=-7.00000e-01, resind= 4, atomnumber= 7}
40: atom[ 81]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.40000e-01, mB= 1.00800e+00, qB= 4.40000e-01, resind= 4, atomnumber= 1}
40: atom[ 82]={type= 8, typeB= 8, ptype= Atom, m= 1.20110e+01, q= 6.40000e-01, mB= 1.20110e+01, qB= 6.40000e-01, resind= 4, atomnumber= 6}
40: atom[ 83]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7}
40: atom[ 84]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1}
40: atom[ 85]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1}
40: atom[ 86]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7}
40: atom[ 87]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1}
40: atom[ 88]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1}
40: atom[ 89]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 4, atomnumber= 6}
40: atom[ 90]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 4, atomnumber= 8}
40: atom[ 91]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 5, atomnumber= 7}
40: atom[ 92]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 5, atomnumber= 1}
40: atom[ 93]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 5, atomnumber= 6}
40: atom[ 94]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1}
40: atom[ 95]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 6.00000e-02, mB= 1.20110e+01, qB= 6.00000e-02, resind= 5, atomnumber= 6}
40: atom[ 96]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1}
40: atom[ 97]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1}
40: atom[ 98]={type= 9, typeB= 9, ptype= Atom, m= 3.20600e+01, q=-3.35000e-01, mB= 3.20600e+01, qB=-3.35000e-01, resind= 5, atomnumber= 16}
40: atom[ 99]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 1.55000e-01, mB= 1.00800e+00, qB= 1.55000e-01, resind= 5, atomnumber= 1}
40: atom[ 100]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 5, atomnumber= 6}
40: atom[ 101]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 5, atomnumber= 8}
40: atom[ 102]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 6, atomnumber= 7}
40: atom[ 103]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 6, atomnumber= 1}
40: atom[ 104]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 6, atomnumber= 6}
40: atom[ 105]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1}
40: atom[ 106]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 6, atomnumber= 6}
40: atom[ 107]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1}
40: atom[ 108]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1}
40: atom[ 109]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-2.20000e-01, mB= 1.20110e+01, qB=-2.20000e-01, resind= 6, atomnumber= 6}
40: atom[ 110]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1}
40: atom[ 111]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1}
40: atom[ 112]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 7.00000e-01, mB= 1.20110e+01, qB= 7.00000e-01, resind= 6, atomnumber= 6}
40: atom[ 113]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8}
40: atom[ 114]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8}
40: atom[ 115]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 6, atomnumber= 6}
40: atom[ 116]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 6, atomnumber= 8}
40: atom[ 117]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 7, atomnumber= 7}
40: atom[ 118]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 7, atomnumber= 1}
40: atom[ 119]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 7, atomnumber= 6}
40: atom[ 120]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
40: atom[ 121]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 7, atomnumber= 6}
40: atom[ 122]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
40: atom[ 123]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
40: atom[ 124]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 7, atomnumber= 6}
40: atom[ 125]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
40: atom[ 126]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6}
40: atom[ 127]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
40: atom[ 128]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
40: atom[ 129]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
40: atom[ 130]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6}
40: atom[ 131]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
40: atom[ 132]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
40: atom[ 133]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
40: atom[ 134]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 7, atomnumber= 6}
40: atom[ 135]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 7, atomnumber= 8}
40: atom[ 136]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 8, atomnumber= 7}
40: atom[ 137]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 8, atomnumber= 1}
40: atom[ 138]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 8, atomnumber= 6}
40: atom[ 139]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1}
40: atom[ 140]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 8, atomnumber= 6}
40: atom[ 141]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1}
40: atom[ 142]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1}
40: atom[ 143]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1}
40: atom[ 144]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 8, atomnumber= 6}
40: atom[ 145]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 8, atomnumber= 8}
40: atom[ 146]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 9, atomnumber= 7}
40: atom[ 147]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 9, atomnumber= 1}
40: atom[ 148]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 9, atomnumber= 6}
40: atom[ 149]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1}
40: atom[ 150]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 9, atomnumber= 6}
40: atom[ 151]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1}
40: atom[ 152]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1}
40: atom[ 153]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1}
40: atom[ 154]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 9, atomnumber= 6}
40: atom[ 155]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 9, atomnumber= 8}
40: atom (156):
40: atom[0]={name="N"}
40: atom[1]={name="H1"}
40: atom[2]={name="H2"}
40: atom[3]={name="H3"}
40: atom[4]={name="CA"}
40: atom[5]={name="HA"}
40: atom[6]={name="CB"}
40: atom[7]={name="HB1"}
40: atom[8]={name="HB2"}
40: atom[9]={name="CG"}
40: atom[10]={name="HG1"}
40: atom[11]={name="HG2"}
40: atom[12]={name="CD"}
40: atom[13]={name="HD1"}
40: atom[14]={name="HD2"}
40: atom[15]={name="CE"}
40: atom[16]={name="HE1"}
40: atom[17]={name="HE2"}
40: atom[18]={name="NZ"}
40: atom[19]={name="HZ1"}
40: atom[20]={name="HZ2"}
40: atom[21]={name="HZ3"}
40: atom[22]={name="C"}
40: atom[23]={name="O"}
40: atom[24]={name="N"}
40: atom[25]={name="H"}
40: atom[26]={name="CA"}
40: atom[27]={name="HA"}
40: atom[28]={name="CB"}
40: atom[29]={name="HB"}
40: atom[30]={name="CG1"}
40: atom[31]={name="HG11"}
40: atom[32]={name="HG12"}
40: atom[33]={name="HG13"}
40: atom[34]={name="CG2"}
40: atom[35]={name="HG21"}
40: atom[36]={name="HG22"}
40: atom[37]={name="HG23"}
40: atom[38]={name="C"}
40: atom[39]={name="O"}
40: atom[40]={name="N"}
40: atom[41]={name="H"}
40: atom[42]={name="CA"}
40: atom[43]={name="HA"}
40: atom[44]={name="CB"}
40: atom[45]={name="HB1"}
40: atom[46]={name="HB2"}
40: atom[47]={name="CG"}
40: atom[48]={name="CD1"}
40: atom[49]={name="HD1"}
40: atom[50]={name="CD2"}
40: atom[51]={name="HD2"}
40: atom[52]={name="CE1"}
40: atom[53]={name="HE1"}
40: atom[54]={name="CE2"}
40: atom[55]={name="HE2"}
40: atom[56]={name="CZ"}
40: atom[57]={name="HZ"}
40: atom[58]={name="C"}
40: atom[59]={name="O"}
40: atom[60]={name="N"}
40: atom[61]={name="H"}
40: atom[62]={name="CA"}
40: atom[63]={name="HA1"}
40: atom[64]={name="HA2"}
40: atom[65]={name="C"}
40: atom[66]={name="O"}
40: atom[67]={name="N"}
40: atom[68]={name="H"}
40: atom[69]={name="CA"}
40: atom[70]={name="HA"}
40: atom[71]={name="CB"}
40: atom[72]={name="HB1"}
40: atom[73]={name="HB2"}
40: atom[74]={name="CG"}
40: atom[75]={name="HG1"}
40: atom[76]={name="HG2"}
40: atom[77]={name="CD"}
40: atom[78]={name="HD1"}
40: atom[79]={name="HD2"}
40: atom[80]={name="NE"}
40: atom[81]={name="HE"}
40: atom[82]={name="CZ"}
40: atom[83]={name="NH1"}
40: atom[84]={name="HH11"}
40: atom[85]={name="HH12"}
40: atom[86]={name="NH2"}
40: atom[87]={name="HH21"}
40: atom[88]={name="HH22"}
40: atom[89]={name="C"}
40: atom[90]={name="O"}
40: atom[91]={name="N"}
40: atom[92]={name="H"}
40: atom[93]={name="CA"}
40: atom[94]={name="HA"}
40: atom[95]={name="CB"}
40: atom[96]={name="HB1"}
40: atom[97]={name="HB2"}
40: atom[98]={name="SG"}
40: atom[99]={name="HG"}
40: atom[100]={name="C"}
40: atom[101]={name="O"}
40: atom[102]={name="N"}
40: atom[103]={name="H"}
40: atom[104]={name="CA"}
40: atom[105]={name="HA"}
40: atom[106]={name="CB"}
40: atom[107]={name="HB1"}
40: atom[108]={name="HB2"}
40: atom[109]={name="CG"}
40: atom[110]={name="HG1"}
40: atom[111]={name="HG2"}
40: atom[112]={name="CD"}
40: atom[113]={name="OE1"}
40: atom[114]={name="OE2"}
40: atom[115]={name="C"}
40: atom[116]={name="O"}
40: atom[117]={name="N"}
40: atom[118]={name="H"}
40: atom[119]={name="CA"}
40: atom[120]={name="HA"}
40: atom[121]={name="CB"}
40: atom[122]={name="HB1"}
40: atom[123]={name="HB2"}
40: atom[124]={name="CG"}
40: atom[125]={name="HG"}
40: atom[126]={name="CD1"}
40: atom[127]={name="HD11"}
40: atom[128]={name="HD12"}
40: atom[129]={name="HD13"}
40: atom[130]={name="CD2"}
40: atom[131]={name="HD21"}
40: atom[132]={name="HD22"}
40: atom[133]={name="HD23"}
40: atom[134]={name="C"}
40: atom[135]={name="O"}
40: atom[136]={name="N"}
40: atom[137]={name="H"}
40: atom[138]={name="CA"}
40: atom[139]={name="HA"}
40: atom[140]={name="CB"}
40: atom[141]={name="HB1"}
40: atom[142]={name="HB2"}
40: atom[143]={name="HB3"}
40: atom[144]={name="C"}
40: atom[145]={name="O"}
40: atom[146]={name="N"}
40: atom[147]={name="H"}
40: atom[148]={name="CA"}
40: atom[149]={name="HA"}
40: atom[150]={name="CB"}
40: atom[151]={name="HB1"}
40: atom[152]={name="HB2"}
40: atom[153]={name="HB3"}
40: atom[154]={name="C"}
40: atom[155]={name="O"}
40: type (156):
40: type[0]={name="opls_287",nameB="opls_287"}
40: type[1]={name="opls_290",nameB="opls_290"}
40: type[2]={name="opls_290",nameB="opls_290"}
40: type[3]={name="opls_290",nameB="opls_290"}
40: type[4]={name="opls_293B",nameB="opls_293B"}
40: type[5]={name="opls_140",nameB="opls_140"}
40: type[6]={name="opls_136",nameB="opls_136"}
40: type[7]={name="opls_140",nameB="opls_140"}
40: type[8]={name="opls_140",nameB="opls_140"}
40: type[9]={name="opls_136",nameB="opls_136"}
40: type[10]={name="opls_140",nameB="opls_140"}
40: type[11]={name="opls_140",nameB="opls_140"}
40: type[12]={name="opls_136",nameB="opls_136"}
40: type[13]={name="opls_140",nameB="opls_140"}
40: type[14]={name="opls_140",nameB="opls_140"}
40: type[15]={name="opls_292",nameB="opls_292"}
40: type[16]={name="opls_140",nameB="opls_140"}
40: type[17]={name="opls_140",nameB="opls_140"}
40: type[18]={name="opls_287",nameB="opls_287"}
40: type[19]={name="opls_290",nameB="opls_290"}
40: type[20]={name="opls_290",nameB="opls_290"}
40: type[21]={name="opls_290",nameB="opls_290"}
40: type[22]={name="opls_235",nameB="opls_235"}
40: type[23]={name="opls_236",nameB="opls_236"}
40: type[24]={name="opls_238",nameB="opls_238"}
40: type[25]={name="opls_241",nameB="opls_241"}
40: type[26]={name="opls_224B",nameB="opls_224B"}
40: type[27]={name="opls_140",nameB="opls_140"}
40: type[28]={name="opls_137",nameB="opls_137"}
40: type[29]={name="opls_140",nameB="opls_140"}
40: type[30]={name="opls_135",nameB="opls_135"}
40: type[31]={name="opls_140",nameB="opls_140"}
40: type[32]={name="opls_140",nameB="opls_140"}
40: type[33]={name="opls_140",nameB="opls_140"}
40: type[34]={name="opls_135",nameB="opls_135"}
40: type[35]={name="opls_140",nameB="opls_140"}
40: type[36]={name="opls_140",nameB="opls_140"}
40: type[37]={name="opls_140",nameB="opls_140"}
40: type[38]={name="opls_235",nameB="opls_235"}
40: type[39]={name="opls_236",nameB="opls_236"}
40: type[40]={name="opls_238",nameB="opls_238"}
40: type[41]={name="opls_241",nameB="opls_241"}
40: type[42]={name="opls_224B",nameB="opls_224B"}
40: type[43]={name="opls_140",nameB="opls_140"}
40: type[44]={name="opls_149",nameB="opls_149"}
40: type[45]={name="opls_140",nameB="opls_140"}
40: type[46]={name="opls_140",nameB="opls_140"}
40: type[47]={name="opls_145",nameB="opls_145"}
40: type[48]={name="opls_145",nameB="opls_145"}
40: type[49]={name="opls_146",nameB="opls_146"}
40: type[50]={name="opls_145",nameB="opls_145"}
40: type[51]={name="opls_146",nameB="opls_146"}
40: type[52]={name="opls_145",nameB="opls_145"}
40: type[53]={name="opls_146",nameB="opls_146"}
40: type[54]={name="opls_145",nameB="opls_145"}
40: type[55]={name="opls_146",nameB="opls_146"}
40: type[56]={name="opls_145",nameB="opls_145"}
40: type[57]={name="opls_146",nameB="opls_146"}
40: type[58]={name="opls_235",nameB="opls_235"}
40: type[59]={name="opls_236",nameB="opls_236"}
40: type[60]={name="opls_238",nameB="opls_238"}
40: type[61]={name="opls_241",nameB="opls_241"}
40: type[62]={name="opls_223B",nameB="opls_223B"}
40: type[63]={name="opls_140",nameB="opls_140"}
40: type[64]={name="opls_140",nameB="opls_140"}
40: type[65]={name="opls_235",nameB="opls_235"}
40: type[66]={name="opls_236",nameB="opls_236"}
40: type[67]={name="opls_238",nameB="opls_238"}
40: type[68]={name="opls_241",nameB="opls_241"}
40: type[69]={name="opls_224B",nameB="opls_224B"}
40: type[70]={name="opls_140",nameB="opls_140"}
40: type[71]={name="opls_136",nameB="opls_136"}
40: type[72]={name="opls_140",nameB="opls_140"}
40: type[73]={name="opls_140",nameB="opls_140"}
40: type[74]={name="opls_308",nameB="opls_308"}
40: type[75]={name="opls_140",nameB="opls_140"}
40: type[76]={name="opls_140",nameB="opls_140"}
40: type[77]={name="opls_307",nameB="opls_307"}
40: type[78]={name="opls_140",nameB="opls_140"}
40: type[79]={name="opls_140",nameB="opls_140"}
40: type[80]={name="opls_303",nameB="opls_303"}
40: type[81]={name="opls_304",nameB="opls_304"}
40: type[82]={name="opls_302",nameB="opls_302"}
40: type[83]={name="opls_300",nameB="opls_300"}
40: type[84]={name="opls_301",nameB="opls_301"}
40: type[85]={name="opls_301",nameB="opls_301"}
40: type[86]={name="opls_300",nameB="opls_300"}
40: type[87]={name="opls_301",nameB="opls_301"}
40: type[88]={name="opls_301",nameB="opls_301"}
40: type[89]={name="opls_235",nameB="opls_235"}
40: type[90]={name="opls_236",nameB="opls_236"}
40: type[91]={name="opls_238",nameB="opls_238"}
40: type[92]={name="opls_241",nameB="opls_241"}
40: type[93]={name="opls_224B",nameB="opls_224B"}
40: type[94]={name="opls_140",nameB="opls_140"}
40: type[95]={name="opls_206",nameB="opls_206"}
40: type[96]={name="opls_140",nameB="opls_140"}
40: type[97]={name="opls_140",nameB="opls_140"}
40: type[98]={name="opls_200",nameB="opls_200"}
40: type[99]={name="opls_204",nameB="opls_204"}
40: type[100]={name="opls_235",nameB="opls_235"}
40: type[101]={name="opls_236",nameB="opls_236"}
40: type[102]={name="opls_238",nameB="opls_238"}
40: type[103]={name="opls_241",nameB="opls_241"}
40: type[104]={name="opls_224B",nameB="opls_224B"}
40: type[105]={name="opls_140",nameB="opls_140"}
40: type[106]={name="opls_136",nameB="opls_136"}
40: type[107]={name="opls_140",nameB="opls_140"}
40: type[108]={name="opls_140",nameB="opls_140"}
40: type[109]={name="opls_274",nameB="opls_274"}
40: type[110]={name="opls_140",nameB="opls_140"}
40: type[111]={name="opls_140",nameB="opls_140"}
40: type[112]={name="opls_271",nameB="opls_271"}
40: type[113]={name="opls_272",nameB="opls_272"}
40: type[114]={name="opls_272",nameB="opls_272"}
40: type[115]={name="opls_235",nameB="opls_235"}
40: type[116]={name="opls_236",nameB="opls_236"}
40: type[117]={name="opls_238",nameB="opls_238"}
40: type[118]={name="opls_241",nameB="opls_241"}
40: type[119]={name="opls_224B",nameB="opls_224B"}
40: type[120]={name="opls_140",nameB="opls_140"}
40: type[121]={name="opls_136",nameB="opls_136"}
40: type[122]={name="opls_140",nameB="opls_140"}
40: type[123]={name="opls_140",nameB="opls_140"}
40: type[124]={name="opls_137",nameB="opls_137"}
40: type[125]={name="opls_140",nameB="opls_140"}
40: type[126]={name="opls_135",nameB="opls_135"}
40: type[127]={name="opls_140",nameB="opls_140"}
40: type[128]={name="opls_140",nameB="opls_140"}
40: type[129]={name="opls_140",nameB="opls_140"}
40: type[130]={name="opls_135",nameB="opls_135"}
40: type[131]={name="opls_140",nameB="opls_140"}
40: type[132]={name="opls_140",nameB="opls_140"}
40: type[133]={name="opls_140",nameB="opls_140"}
40: type[134]={name="opls_235",nameB="opls_235"}
40: type[135]={name="opls_236",nameB="opls_236"}
40: type[136]={name="opls_238",nameB="opls_238"}
40: type[137]={name="opls_241",nameB="opls_241"}
40: type[138]={name="opls_224B",nameB="opls_224B"}
40: type[139]={name="opls_140",nameB="opls_140"}
40: type[140]={name="opls_135",nameB="opls_135"}
40: type[141]={name="opls_140",nameB="opls_140"}
40: type[142]={name="opls_140",nameB="opls_140"}
40: type[143]={name="opls_140",nameB="opls_140"}
40: type[144]={name="opls_235",nameB="opls_235"}
40: type[145]={name="opls_236",nameB="opls_236"}
40: type[146]={name="opls_238",nameB="opls_238"}
40: type[147]={name="opls_241",nameB="opls_241"}
40: type[148]={name="opls_224B",nameB="opls_224B"}
40: type[149]={name="opls_140",nameB="opls_140"}
40: type[150]={name="opls_135",nameB="opls_135"}
40: type[151]={name="opls_140",nameB="opls_140"}
40: type[152]={name="opls_140",nameB="opls_140"}
40: type[153]={name="opls_140",nameB="opls_140"}
40: type[154]={name="opls_235",nameB="opls_235"}
40: type[155]={name="opls_236",nameB="opls_236"}
40: residue (10):
40: residue[0]={name="LYS", nr=1, ic=' '}
40: residue[1]={name="VAL", nr=2, ic=' '}
40: residue[2]={name="PHE", nr=3, ic=' '}
40: residue[3]={name="GLY", nr=4, ic=' '}
40: residue[4]={name="ARG", nr=5, ic=' '}
40: residue[5]={name="CYS", nr=6, ic=' '}
40: residue[6]={name="GLU", nr=7, ic=' '}
40: residue[7]={name="LEU", nr=8, ic=' '}
40: residue[8]={name="ALA", nr=9, ic=' '}
40: residue[9]={name="ALA", nr=10, ic=' '}
40: excls:
40: nr=156
40: nra=1828
40: excls[0][0..12]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24}
40: excls[1][13..20]={0, 1, 2, 3, 4, 5, 6, 22}
40: excls[2][21..28]={0, 1, 2, 3, 4, 5, 6, 22}
40: excls[3][29..36]={0, 1, 2, 3, 4, 5, 6, 22}
40: excls[4][37..54]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22,
40: 23, 24, 25, 26}
40: excls[5][55..67]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24}
40: excls[6][68..86]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13,
40: 14, 15, 22, 23, 24}
40: excls[7][87..97]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22}
40: excls[8][98..108]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22}
40: excls[9][109..125]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,
40: 16, 17, 18, 22}
40: excls[10][126..136]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15}
40: excls[11][137..147]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15}
40: excls[12][148..164]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16,
40: 17, 18, 19, 20, 21}
40: excls[13][165..175]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18}
40: excls[14][176..186]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18}
40: excls[15][187..200]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18,
40: 19, 20, 21}
40: excls[16][201..211]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21}
40: excls[17][212..222]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21}
40: excls[18][223..233]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21}
40: excls[19][234..241]={12, 15, 16, 17, 18, 19, 20, 21}
40: excls[20][242..249]={12, 15, 16, 17, 18, 19, 20, 21}
40: excls[21][250..257]={12, 15, 16, 17, 18, 19, 20, 21}
40: excls[22][258..275]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24,
40: 25, 26, 27, 28, 38}
40: excls[23][276..284]={0, 4, 5, 6, 22, 23, 24, 25, 26}
40: excls[24][285..301]={0, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29,
40: 30, 34, 38, 39, 40}
40: excls[25][302..310]={4, 22, 23, 24, 25, 26, 27, 28, 38}
40: excls[26][311..332]={4, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31,
40: 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42}
40: excls[27][333..344]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39,
40: 40}
40: excls[28][345..362]={22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33,
40: 34, 35, 36, 37, 38, 39, 40}
40: excls[29][363..376]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,
40: 36, 37, 38}
40: excls[30][377..390]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,
40: 36, 37, 38}
40: excls[31][391..398]={26, 28, 29, 30, 31, 32, 33, 34}
40: excls[32][399..406]={26, 28, 29, 30, 31, 32, 33, 34}
40: excls[33][407..414]={26, 28, 29, 30, 31, 32, 33, 34}
40: excls[34][415..428]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,
40: 36, 37, 38}
40: excls[35][429..436]={26, 28, 29, 30, 34, 35, 36, 37}
40: excls[36][437..444]={26, 28, 29, 30, 34, 35, 36, 37}
40: excls[37][445..452]={26, 28, 29, 30, 34, 35, 36, 37}
40: excls[38][453..469]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39,
40: 40, 41, 42, 43, 44, 58}
40: excls[39][470..478]={24, 26, 27, 28, 38, 39, 40, 41, 42}
40: excls[40][479..495]={24, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44,
40: 45, 46, 47, 58, 59, 60}
40: excls[41][496..504]={26, 38, 39, 40, 41, 42, 43, 44, 58}
40: excls[42][505..522]={26, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47,
40: 48, 50, 58, 59, 60, 61, 62}
40: excls[43][523..534]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59,
40: 60}
40: excls[44][535..552]={38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49,
40: 50, 51, 52, 54, 58, 59, 60}
40: excls[45][553..562]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58}
40: excls[46][563..572]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58}
40: excls[47][573..589]={40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51,
40: 52, 53, 54, 55, 56, 58}
40: excls[48][590..603]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53,
40: 54, 56, 57}
40: excls[49][604..611]={44, 47, 48, 49, 50, 52, 53, 56}
40: excls[50][612..625]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54,
40: 55, 56, 57}
40: excls[51][626..633]={44, 47, 48, 50, 51, 54, 55, 56}
40: excls[52][634..644]={44, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57}
40: excls[53][645..652]={47, 48, 49, 52, 53, 54, 56, 57}
40: excls[54][653..663]={44, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57}
40: excls[55][664..671]={47, 50, 51, 52, 54, 55, 56, 57}
40: excls[56][672..682]={47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57}
40: excls[57][683..690]={48, 50, 52, 53, 54, 55, 56, 57}
40: excls[58][691..707]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59,
40: 60, 61, 62, 63, 64, 65}
40: excls[59][708..716]={40, 42, 43, 44, 58, 59, 60, 61, 62}
40: excls[60][717..730]={40, 42, 43, 44, 58, 59, 60, 61, 62, 63, 64,
40: 65, 66, 67}
40: excls[61][731..739]={42, 58, 59, 60, 61, 62, 63, 64, 65}
40: excls[62][740..752]={42, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67,
40: 68, 69}
40: excls[63][753..761]={58, 60, 61, 62, 63, 64, 65, 66, 67}
40: excls[64][762..770]={58, 60, 61, 62, 63, 64, 65, 66, 67}
40: excls[65][771..784]={58, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69,
40: 70, 71, 89}
40: excls[66][785..793]={60, 62, 63, 64, 65, 66, 67, 68, 69}
40: excls[67][794..810]={60, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71,
40: 72, 73, 74, 89, 90, 91}
40: excls[68][811..819]={62, 65, 66, 67, 68, 69, 70, 71, 89}
40: excls[69][820..838]={62, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74,
40: 75, 76, 77, 89, 90, 91, 92, 93}
40: excls[70][839..850]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90,
40: 91}
40: excls[71][851..868]={65, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76,
40: 77, 78, 79, 80, 89, 90, 91}
40: excls[72][869..879]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89}
40: excls[73][880..890]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89}
40: excls[74][891..906]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78,
40: 79, 80, 81, 82, 89}
40: excls[75][907..917]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80}
40: excls[76][918..928]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80}
40: excls[77][929..943]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80,
40: 81, 82, 83, 86}
40: excls[78][944..953]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82}
40: excls[79][954..963]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82}
40: excls[80][964..979]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83,
40: 84, 85, 86, 87, 88}
40: excls[81][980..988]={74, 77, 78, 79, 80, 81, 82, 83, 86}
40: excls[82][989..1001]={74, 77, 78, 79, 80, 81, 82, 83, 84, 85,
40: 86, 87, 88}
40: excls[83][1002..1011]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88}
40: excls[84][1012..1017]={80, 82, 83, 84, 85, 86}
40: excls[85][1018..1023]={80, 82, 83, 84, 85, 86}
40: excls[86][1024..1033]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88}
40: excls[87][1034..1039]={80, 82, 83, 86, 87, 88}
40: excls[88][1040..1045]={80, 82, 83, 86, 87, 88}
40: excls[89][1046..1062]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89,
40: 90, 91, 92, 93, 94, 95, 100}
40: excls[90][1063..1071]={67, 69, 70, 71, 89, 90, 91, 92, 93}
40: excls[91][1072..1088]={67, 69, 70, 71, 89, 90, 91, 92, 93, 94,
40: 95, 96, 97, 98, 100, 101, 102}
40: excls[92][1089..1097]={69, 89, 90, 91, 92, 93, 94, 95, 100}
40: excls[93][1098..1114]={69, 89, 90, 91, 92, 93, 94, 95, 96, 97,
40: 98, 99, 100, 101, 102, 103, 104}
40: excls[94][1115..1126]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100,
40: 101, 102}
40: excls[95][1127..1139]={89, 91, 92, 93, 94, 95, 96, 97, 98, 99,
40: 100, 101, 102}
40: excls[96][1140..1148]={91, 93, 94, 95, 96, 97, 98, 99, 100}
40: excls[97][1149..1157]={91, 93, 94, 95, 96, 97, 98, 99, 100}
40: excls[98][1158..1166]={91, 93, 94, 95, 96, 97, 98, 99, 100}
40: excls[99][1167..1172]={93, 95, 96, 97, 98, 99}
40: excls[100][1173..1189]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100,
40: 101, 102, 103, 104, 105, 106, 115}
40: excls[101][1190..1198]={91, 93, 94, 95, 100, 101, 102, 103, 104}
40: excls[102][1199..1215]={91, 93, 94, 95, 100, 101, 102, 103, 104,
40: 105, 106, 107, 108, 109, 115, 116, 117}
40: excls[103][1216..1224]={93, 100, 101, 102, 103, 104, 105, 106,
40: 115}
40: excls[104][1225..1243]={93, 100, 101, 102, 103, 104, 105, 106,
40: 107, 108, 109, 110, 111, 112, 115, 116, 117, 118, 119}
40: excls[105][1244..1255]={100, 102, 103, 104, 105, 106, 107, 108,
40: 109, 115, 116, 117}
40: excls[106][1256..1272]={100, 102, 103, 104, 105, 106, 107, 108,
40: 109, 110, 111, 112, 113, 114, 115, 116, 117}
40: excls[107][1273..1283]={102, 104, 105, 106, 107, 108, 109, 110,
40: 111, 112, 115}
40: excls[108][1284..1294]={102, 104, 105, 106, 107, 108, 109, 110,
40: 111, 112, 115}
40: excls[109][1295..1307]={102, 104, 105, 106, 107, 108, 109, 110,
40: 111, 112, 113, 114, 115}
40: excls[110][1308..1317]={104, 106, 107, 108, 109, 110, 111, 112,
40: 113, 114}
40: excls[111][1318..1327]={104, 106, 107, 108, 109, 110, 111, 112,
40: 113, 114}
40: excls[112][1328..1337]={104, 106, 107, 108, 109, 110, 111, 112,
40: 113, 114}
40: excls[113][1338..1344]={106, 109, 110, 111, 112, 113, 114}
40: excls[114][1345..1351]={106, 109, 110, 111, 112, 113, 114}
40: excls[115][1352..1368]={100, 102, 103, 104, 105, 106, 107, 108,
40: 109, 115, 116, 117, 118, 119, 120, 121, 134}
40: excls[116][1369..1377]={102, 104, 105, 106, 115, 116, 117, 118,
40: 119}
40: excls[117][1378..1394]={102, 104, 105, 106, 115, 116, 117, 118,
40: 119, 120, 121, 122, 123, 124, 134, 135, 136}
40: excls[118][1395..1403]={104, 115, 116, 117, 118, 119, 120, 121,
40: 134}
40: excls[119][1404..1422]={104, 115, 116, 117, 118, 119, 120, 121,
40: 122, 123, 124, 125, 126, 130, 134, 135, 136, 137, 138}
40: excls[120][1423..1434]={115, 117, 118, 119, 120, 121, 122, 123,
40: 124, 134, 135, 136}
40: excls[121][1435..1455]={115, 117, 118, 119, 120, 121, 122, 123,
40: 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135,
40: 136}
40: excls[122][1456..1466]={117, 119, 120, 121, 122, 123, 124, 125,
40: 126, 130, 134}
40: excls[123][1467..1477]={117, 119, 120, 121, 122, 123, 124, 125,
40: 126, 130, 134}
40: excls[124][1478..1494]={117, 119, 120, 121, 122, 123, 124, 125,
40: 126, 127, 128, 129, 130, 131, 132, 133, 134}
40: excls[125][1495..1508]={119, 121, 122, 123, 124, 125, 126, 127,
40: 128, 129, 130, 131, 132, 133}
40: excls[126][1509..1522]={119, 121, 122, 123, 124, 125, 126, 127,
40: 128, 129, 130, 131, 132, 133}
40: excls[127][1523..1530]={121, 124, 125, 126, 127, 128, 129, 130}
40: excls[128][1531..1538]={121, 124, 125, 126, 127, 128, 129, 130}
40: excls[129][1539..1546]={121, 124, 125, 126, 127, 128, 129, 130}
40: excls[130][1547..1560]={119, 121, 122, 123, 124, 125, 126, 127,
40: 128, 129, 130, 131, 132, 133}
40: excls[131][1561..1568]={121, 124, 125, 126, 130, 131, 132, 133}
40: excls[132][1569..1576]={121, 124, 125, 126, 130, 131, 132, 133}
40: excls[133][1577..1584]={121, 124, 125, 126, 130, 131, 132, 133}
40: excls[134][1585..1601]={115, 117, 118, 119, 120, 121, 122, 123,
40: 124, 134, 135, 136, 137, 138, 139, 140, 144}
40: excls[135][1602..1610]={117, 119, 120, 121, 134, 135, 136, 137,
40: 138}
40: excls[136][1611..1627]={117, 119, 120, 121, 134, 135, 136, 137,
40: 138, 139, 140, 141, 142, 143, 144, 145, 146}
40: excls[137][1628..1636]={119, 134, 135, 136, 137, 138, 139, 140,
40: 144}
40: excls[138][1637..1652]={119, 134, 135, 136, 137, 138, 139, 140,
40: 141, 142, 143, 144, 145, 146, 147, 148}
40: excls[139][1653..1664]={134, 136, 137, 138, 139, 140, 141, 142,
40: 143, 144, 145, 146}
40: excls[140][1665..1676]={134, 136, 137, 138, 139, 140, 141, 142,
40: 143, 144, 145, 146}
40: excls[141][1677..1684]={136, 138, 139, 140, 141, 142, 143, 144}
40: excls[142][1685..1692]={136, 138, 139, 140, 141, 142, 143, 144}
40: excls[143][1693..1700]={136, 138, 139, 140, 141, 142, 143, 144}
40: excls[144][1701..1717]={134, 136, 137, 138, 139, 140, 141, 142,
40: 143, 144, 145, 146, 147, 148, 149, 150, 154}
40: excls[145][1718..1726]={136, 138, 139, 140, 144, 145, 146, 147,
40: 148}
40: excls[146][1727..1742]={136, 138, 139, 140, 144, 145, 146, 147,
40: 148, 149, 150, 151, 152, 153, 154, 155}
40: excls[147][1743..1751]={138, 144, 145, 146, 147, 148, 149, 150,
40: 154}
40: excls[148][1752..1764]={138, 144, 145, 146, 147, 148, 149, 150,
40: 151, 152, 153, 154, 155}
40: excls[149][1765..1775]={144, 146, 147, 148, 149, 150, 151, 152,
40: 153, 154, 155}
40: excls[150][1776..1786]={144, 146, 147, 148, 149, 150, 151, 152,
40: 153, 154, 155}
40: excls[151][1787..1794]={146, 148, 149, 150, 151, 152, 153, 154}
40: excls[152][1795..1802]={146, 148, 149, 150, 151, 152, 153, 154}
40: excls[153][1803..1810]={146, 148, 149, 150, 151, 152, 153, 154}
40: excls[154][1811..1821]={144, 146, 147, 148, 149, 150, 151, 152,
40: 153, 154, 155}
40: excls[155][1822..1827]={146, 148, 149, 150, 154, 155}
40: Bond:
40: nr: 468
40: iatoms:
40: 0 type=100 (BONDS) 0 1
40: 1 type=100 (BONDS) 0 2
40: 2 type=100 (BONDS) 0 3
40: 3 type=101 (BONDS) 0 4
40: 4 type=102 (BONDS) 4 5
40: 5 type=103 (BONDS) 4 6
40: 6 type=104 (BONDS) 4 22
40: 7 type=102 (BONDS) 6 7
40: 8 type=102 (BONDS) 6 8
40: 9 type=103 (BONDS) 6 9
40: 10 type=102 (BONDS) 9 10
40: 11 type=102 (BONDS) 9 11
40: 12 type=103 (BONDS) 9 12
40: 13 type=102 (BONDS) 12 13
40: 14 type=102 (BONDS) 12 14
40: 15 type=103 (BONDS) 12 15
40: 16 type=102 (BONDS) 15 16
40: 17 type=102 (BONDS) 15 17
40: 18 type=101 (BONDS) 15 18
40: 19 type=100 (BONDS) 18 19
40: 20 type=100 (BONDS) 18 20
40: 21 type=100 (BONDS) 18 21
40: 22 type=105 (BONDS) 22 23
40: 23 type=106 (BONDS) 22 24
40: 24 type=100 (BONDS) 24 25
40: 25 type=107 (BONDS) 24 26
40: 26 type=102 (BONDS) 26 27
40: 27 type=103 (BONDS) 26 28
40: 28 type=104 (BONDS) 26 38
40: 29 type=102 (BONDS) 28 29
40: 30 type=103 (BONDS) 28 30
40: 31 type=103 (BONDS) 28 34
40: 32 type=102 (BONDS) 30 31
40: 33 type=102 (BONDS) 30 32
40: 34 type=102 (BONDS) 30 33
40: 35 type=102 (BONDS) 34 35
40: 36 type=102 (BONDS) 34 36
40: 37 type=102 (BONDS) 34 37
40: 38 type=105 (BONDS) 38 39
40: 39 type=106 (BONDS) 38 40
40: 40 type=100 (BONDS) 40 41
40: 41 type=107 (BONDS) 40 42
40: 42 type=102 (BONDS) 42 43
40: 43 type=103 (BONDS) 42 44
40: 44 type=104 (BONDS) 42 58
40: 45 type=102 (BONDS) 44 45
40: 46 type=102 (BONDS) 44 46
40: 47 type=108 (BONDS) 44 47
40: 48 type=109 (BONDS) 47 48
40: 49 type=109 (BONDS) 47 50
40: 50 type=110 (BONDS) 48 49
40: 51 type=109 (BONDS) 48 52
40: 52 type=110 (BONDS) 50 51
40: 53 type=109 (BONDS) 50 54
40: 54 type=110 (BONDS) 52 53
40: 55 type=109 (BONDS) 52 56
40: 56 type=110 (BONDS) 54 55
40: 57 type=109 (BONDS) 54 56
40: 58 type=110 (BONDS) 56 57
40: 59 type=105 (BONDS) 58 59
40: 60 type=106 (BONDS) 58 60
40: 61 type=100 (BONDS) 60 61
40: 62 type=107 (BONDS) 60 62
40: 63 type=102 (BONDS) 62 63
40: 64 type=102 (BONDS) 62 64
40: 65 type=104 (BONDS) 62 65
40: 66 type=105 (BONDS) 65 66
40: 67 type=106 (BONDS) 65 67
40: 68 type=100 (BONDS) 67 68
40: 69 type=107 (BONDS) 67 69
40: 70 type=102 (BONDS) 69 70
40: 71 type=103 (BONDS) 69 71
40: 72 type=104 (BONDS) 69 89
40: 73 type=102 (BONDS) 71 72
40: 74 type=102 (BONDS) 71 73
40: 75 type=103 (BONDS) 71 74
40: 76 type=102 (BONDS) 74 75
40: 77 type=102 (BONDS) 74 76
40: 78 type=103 (BONDS) 74 77
40: 79 type=102 (BONDS) 77 78
40: 80 type=102 (BONDS) 77 79
40: 81 type=111 (BONDS) 77 80
40: 82 type=100 (BONDS) 80 81
40: 83 type=112 (BONDS) 80 82
40: 84 type=112 (BONDS) 82 83
40: 85 type=112 (BONDS) 82 86
40: 86 type=100 (BONDS) 83 84
40: 87 type=100 (BONDS) 83 85
40: 88 type=100 (BONDS) 86 87
40: 89 type=100 (BONDS) 86 88
40: 90 type=105 (BONDS) 89 90
40: 91 type=106 (BONDS) 89 91
40: 92 type=100 (BONDS) 91 92
40: 93 type=107 (BONDS) 91 93
40: 94 type=102 (BONDS) 93 94
40: 95 type=103 (BONDS) 93 95
40: 96 type=104 (BONDS) 93 100
40: 97 type=102 (BONDS) 95 96
40: 98 type=102 (BONDS) 95 97
40: 99 type=113 (BONDS) 95 98
40: 100 type=114 (BONDS) 98 99
40: 101 type=105 (BONDS) 100 101
40: 102 type=106 (BONDS) 100 102
40: 103 type=100 (BONDS) 102 103
40: 104 type=107 (BONDS) 102 104
40: 105 type=102 (BONDS) 104 105
40: 106 type=103 (BONDS) 104 106
40: 107 type=104 (BONDS) 104 115
40: 108 type=102 (BONDS) 106 107
40: 109 type=102 (BONDS) 106 108
40: 110 type=103 (BONDS) 106 109
40: 111 type=102 (BONDS) 109 110
40: 112 type=102 (BONDS) 109 111
40: 113 type=104 (BONDS) 109 112
40: 114 type=115 (BONDS) 112 113
40: 115 type=115 (BONDS) 112 114
40: 116 type=105 (BONDS) 115 116
40: 117 type=106 (BONDS) 115 117
40: 118 type=100 (BONDS) 117 118
40: 119 type=107 (BONDS) 117 119
40: 120 type=102 (BONDS) 119 120
40: 121 type=103 (BONDS) 119 121
40: 122 type=104 (BONDS) 119 134
40: 123 type=102 (BONDS) 121 122
40: 124 type=102 (BONDS) 121 123
40: 125 type=103 (BONDS) 121 124
40: 126 type=102 (BONDS) 124 125
40: 127 type=103 (BONDS) 124 126
40: 128 type=103 (BONDS) 124 130
40: 129 type=102 (BONDS) 126 127
40: 130 type=102 (BONDS) 126 128
40: 131 type=102 (BONDS) 126 129
40: 132 type=102 (BONDS) 130 131
40: 133 type=102 (BONDS) 130 132
40: 134 type=102 (BONDS) 130 133
40: 135 type=105 (BONDS) 134 135
40: 136 type=106 (BONDS) 134 136
40: 137 type=100 (BONDS) 136 137
40: 138 type=107 (BONDS) 136 138
40: 139 type=102 (BONDS) 138 139
40: 140 type=103 (BONDS) 138 140
40: 141 type=104 (BONDS) 138 144
40: 142 type=102 (BONDS) 140 141
40: 143 type=102 (BONDS) 140 142
40: 144 type=102 (BONDS) 140 143
40: 145 type=105 (BONDS) 144 145
40: 146 type=106 (BONDS) 144 146
40: 147 type=100 (BONDS) 146 147
40: 148 type=107 (BONDS) 146 148
40: 149 type=102 (BONDS) 148 149
40: 150 type=103 (BONDS) 148 150
40: 151 type=104 (BONDS) 148 154
40: 152 type=102 (BONDS) 150 151
40: 153 type=102 (BONDS) 150 152
40: 154 type=102 (BONDS) 150 153
40: 155 type=105 (BONDS) 154 155
40: G96Bond:
40: nr: 0
40: Morse:
40: nr: 0
40: Cubic Bonds:
40: nr: 0
40: Connect Bonds:
40: nr: 0
40: Harmonic Pot.:
40: nr: 0
40: FENE Bonds:
40: nr: 0
40: Tab. Bonds:
40: nr: 0
40: Tab. Bonds NC:
40: nr: 0
40: Restraint Pot.:
40: nr: 0
40: Angle:
40: nr: 1124
40: iatoms:
40: 0 type=116 (ANGLES) 1 0 2
40: 1 type=116 (ANGLES) 1 0 3
40: 2 type=116 (ANGLES) 1 0 4
40: 3 type=116 (ANGLES) 2 0 3
40: 4 type=116 (ANGLES) 2 0 4
40: 5 type=116 (ANGLES) 3 0 4
40: 6 type=116 (ANGLES) 0 4 5
40: 7 type=117 (ANGLES) 0 4 6
40: 8 type=117 (ANGLES) 0 4 22
40: 9 type=118 (ANGLES) 5 4 6
40: 10 type=116 (ANGLES) 5 4 22
40: 11 type=119 (ANGLES) 6 4 22
40: 12 type=118 (ANGLES) 4 6 7
40: 13 type=118 (ANGLES) 4 6 8
40: 14 type=120 (ANGLES) 4 6 9
40: 15 type=121 (ANGLES) 7 6 8
40: 16 type=118 (ANGLES) 7 6 9
40: 17 type=118 (ANGLES) 8 6 9
40: 18 type=118 (ANGLES) 6 9 10
40: 19 type=118 (ANGLES) 6 9 11
40: 20 type=120 (ANGLES) 6 9 12
40: 21 type=121 (ANGLES) 10 9 11
40: 22 type=118 (ANGLES) 10 9 12
40: 23 type=118 (ANGLES) 11 9 12
40: 24 type=118 (ANGLES) 9 12 13
40: 25 type=118 (ANGLES) 9 12 14
40: 26 type=120 (ANGLES) 9 12 15
40: 27 type=121 (ANGLES) 13 12 14
40: 28 type=118 (ANGLES) 13 12 15
40: 29 type=118 (ANGLES) 14 12 15
40: 30 type=118 (ANGLES) 12 15 16
40: 31 type=118 (ANGLES) 12 15 17
40: 32 type=117 (ANGLES) 12 15 18
40: 33 type=121 (ANGLES) 16 15 17
40: 34 type=116 (ANGLES) 16 15 18
40: 35 type=116 (ANGLES) 17 15 18
40: 36 type=116 (ANGLES) 15 18 19
40: 37 type=116 (ANGLES) 15 18 20
40: 38 type=116 (ANGLES) 15 18 21
40: 39 type=116 (ANGLES) 19 18 20
40: 40 type=116 (ANGLES) 19 18 21
40: 41 type=116 (ANGLES) 20 18 21
40: 42 type=122 (ANGLES) 4 22 23
40: 43 type=123 (ANGLES) 4 22 24
40: 44 type=124 (ANGLES) 23 22 24
40: 45 type=125 (ANGLES) 22 24 25
40: 46 type=126 (ANGLES) 22 24 26
40: 47 type=127 (ANGLES) 25 24 26
40: 48 type=116 (ANGLES) 24 26 27
40: 49 type=128 (ANGLES) 24 26 28
40: 50 type=129 (ANGLES) 24 26 38
40: 51 type=118 (ANGLES) 27 26 28
40: 52 type=116 (ANGLES) 27 26 38
40: 53 type=119 (ANGLES) 28 26 38
40: 54 type=118 (ANGLES) 26 28 29
40: 55 type=120 (ANGLES) 26 28 30
40: 56 type=120 (ANGLES) 26 28 34
40: 57 type=118 (ANGLES) 29 28 30
40: 58 type=118 (ANGLES) 29 28 34
40: 59 type=120 (ANGLES) 30 28 34
40: 60 type=118 (ANGLES) 28 30 31
40: 61 type=118 (ANGLES) 28 30 32
40: 62 type=118 (ANGLES) 28 30 33
40: 63 type=121 (ANGLES) 31 30 32
40: 64 type=121 (ANGLES) 31 30 33
40: 65 type=121 (ANGLES) 32 30 33
40: 66 type=118 (ANGLES) 28 34 35
40: 67 type=118 (ANGLES) 28 34 36
40: 68 type=118 (ANGLES) 28 34 37
40: 69 type=121 (ANGLES) 35 34 36
40: 70 type=121 (ANGLES) 35 34 37
40: 71 type=121 (ANGLES) 36 34 37
40: 72 type=122 (ANGLES) 26 38 39
40: 73 type=123 (ANGLES) 26 38 40
40: 74 type=124 (ANGLES) 39 38 40
40: 75 type=125 (ANGLES) 38 40 41
40: 76 type=126 (ANGLES) 38 40 42
40: 77 type=127 (ANGLES) 41 40 42
40: 78 type=116 (ANGLES) 40 42 43
40: 79 type=128 (ANGLES) 40 42 44
40: 80 type=129 (ANGLES) 40 42 58
40: 81 type=118 (ANGLES) 43 42 44
40: 82 type=116 (ANGLES) 43 42 58
40: 83 type=119 (ANGLES) 44 42 58
40: 84 type=118 (ANGLES) 42 44 45
40: 85 type=118 (ANGLES) 42 44 46
40: 86 type=130 (ANGLES) 42 44 47
40: 87 type=121 (ANGLES) 45 44 46
40: 88 type=116 (ANGLES) 45 44 47
40: 89 type=116 (ANGLES) 46 44 47
40: 90 type=131 (ANGLES) 44 47 48
40: 91 type=131 (ANGLES) 44 47 50
40: 92 type=132 (ANGLES) 48 47 50
40: 93 type=133 (ANGLES) 47 48 49
40: 94 type=132 (ANGLES) 47 48 52
40: 95 type=133 (ANGLES) 49 48 52
40: 96 type=133 (ANGLES) 47 50 51
40: 97 type=132 (ANGLES) 47 50 54
40: 98 type=133 (ANGLES) 51 50 54
40: 99 type=133 (ANGLES) 48 52 53
40: 100 type=132 (ANGLES) 48 52 56
40: 101 type=133 (ANGLES) 53 52 56
40: 102 type=133 (ANGLES) 50 54 55
40: 103 type=132 (ANGLES) 50 54 56
40: 104 type=133 (ANGLES) 55 54 56
40: 105 type=132 (ANGLES) 52 56 54
40: 106 type=133 (ANGLES) 52 56 57
40: 107 type=133 (ANGLES) 54 56 57
40: 108 type=122 (ANGLES) 42 58 59
40: 109 type=123 (ANGLES) 42 58 60
40: 110 type=124 (ANGLES) 59 58 60
40: 111 type=125 (ANGLES) 58 60 61
40: 112 type=126 (ANGLES) 58 60 62
40: 113 type=127 (ANGLES) 61 60 62
40: 114 type=116 (ANGLES) 60 62 63
40: 115 type=116 (ANGLES) 60 62 64
40: 116 type=129 (ANGLES) 60 62 65
40: 117 type=121 (ANGLES) 63 62 64
40: 118 type=116 (ANGLES) 63 62 65
40: 119 type=116 (ANGLES) 64 62 65
40: 120 type=122 (ANGLES) 62 65 66
40: 121 type=123 (ANGLES) 62 65 67
40: 122 type=124 (ANGLES) 66 65 67
40: 123 type=125 (ANGLES) 65 67 68
40: 124 type=126 (ANGLES) 65 67 69
40: 125 type=127 (ANGLES) 68 67 69
40: 126 type=116 (ANGLES) 67 69 70
40: 127 type=128 (ANGLES) 67 69 71
40: 128 type=129 (ANGLES) 67 69 89
40: 129 type=118 (ANGLES) 70 69 71
40: 130 type=116 (ANGLES) 70 69 89
40: 131 type=119 (ANGLES) 71 69 89
40: 132 type=118 (ANGLES) 69 71 72
40: 133 type=118 (ANGLES) 69 71 73
40: 134 type=120 (ANGLES) 69 71 74
40: 135 type=121 (ANGLES) 72 71 73
40: 136 type=118 (ANGLES) 72 71 74
40: 137 type=118 (ANGLES) 73 71 74
40: 138 type=118 (ANGLES) 71 74 75
40: 139 type=118 (ANGLES) 71 74 76
40: 140 type=120 (ANGLES) 71 74 77
40: 141 type=121 (ANGLES) 75 74 76
40: 142 type=118 (ANGLES) 75 74 77
40: 143 type=118 (ANGLES) 76 74 77
40: 144 type=118 (ANGLES) 74 77 78
40: 145 type=118 (ANGLES) 74 77 79
40: 146 type=117 (ANGLES) 74 77 80
40: 147 type=121 (ANGLES) 78 77 79
40: 148 type=116 (ANGLES) 78 77 80
40: 149 type=116 (ANGLES) 79 77 80
40: 150 type=134 (ANGLES) 77 80 81
40: 151 type=135 (ANGLES) 77 80 82
40: 152 type=133 (ANGLES) 81 80 82
40: 153 type=131 (ANGLES) 80 82 83
40: 154 type=131 (ANGLES) 80 82 86
40: 155 type=131 (ANGLES) 83 82 86
40: 156 type=133 (ANGLES) 82 83 84
40: 157 type=133 (ANGLES) 82 83 85
40: 158 type=133 (ANGLES) 84 83 85
40: 159 type=133 (ANGLES) 82 86 87
40: 160 type=133 (ANGLES) 82 86 88
40: 161 type=133 (ANGLES) 87 86 88
40: 162 type=122 (ANGLES) 69 89 90
40: 163 type=123 (ANGLES) 69 89 91
40: 164 type=124 (ANGLES) 90 89 91
40: 165 type=125 (ANGLES) 89 91 92
40: 166 type=126 (ANGLES) 89 91 93
40: 167 type=127 (ANGLES) 92 91 93
40: 168 type=116 (ANGLES) 91 93 94
40: 169 type=128 (ANGLES) 91 93 95
40: 170 type=129 (ANGLES) 91 93 100
40: 171 type=118 (ANGLES) 94 93 95
40: 172 type=116 (ANGLES) 94 93 100
40: 173 type=119 (ANGLES) 95 93 100
40: 174 type=118 (ANGLES) 93 95 96
40: 175 type=118 (ANGLES) 93 95 97
40: 176 type=136 (ANGLES) 93 95 98
40: 177 type=121 (ANGLES) 96 95 97
40: 178 type=116 (ANGLES) 96 95 98
40: 179 type=116 (ANGLES) 97 95 98
40: 180 type=137 (ANGLES) 95 98 99
40: 181 type=122 (ANGLES) 93 100 101
40: 182 type=123 (ANGLES) 93 100 102
40: 183 type=124 (ANGLES) 101 100 102
40: 184 type=125 (ANGLES) 100 102 103
40: 185 type=126 (ANGLES) 100 102 104
40: 186 type=127 (ANGLES) 103 102 104
40: 187 type=116 (ANGLES) 102 104 105
40: 188 type=128 (ANGLES) 102 104 106
40: 189 type=129 (ANGLES) 102 104 115
40: 190 type=118 (ANGLES) 105 104 106
40: 191 type=116 (ANGLES) 105 104 115
40: 192 type=119 (ANGLES) 106 104 115
40: 193 type=118 (ANGLES) 104 106 107
40: 194 type=118 (ANGLES) 104 106 108
40: 195 type=120 (ANGLES) 104 106 109
40: 196 type=121 (ANGLES) 107 106 108
40: 197 type=118 (ANGLES) 107 106 109
40: 198 type=118 (ANGLES) 108 106 109
40: 199 type=118 (ANGLES) 106 109 110
40: 200 type=118 (ANGLES) 106 109 111
40: 201 type=119 (ANGLES) 106 109 112
40: 202 type=121 (ANGLES) 110 109 111
40: 203 type=116 (ANGLES) 110 109 112
40: 204 type=116 (ANGLES) 111 109 112
40: 205 type=138 (ANGLES) 109 112 113
40: 206 type=138 (ANGLES) 109 112 114
40: 207 type=139 (ANGLES) 113 112 114
40: 208 type=122 (ANGLES) 104 115 116
40: 209 type=123 (ANGLES) 104 115 117
40: 210 type=124 (ANGLES) 116 115 117
40: 211 type=125 (ANGLES) 115 117 118
40: 212 type=126 (ANGLES) 115 117 119
40: 213 type=127 (ANGLES) 118 117 119
40: 214 type=116 (ANGLES) 117 119 120
40: 215 type=128 (ANGLES) 117 119 121
40: 216 type=129 (ANGLES) 117 119 134
40: 217 type=118 (ANGLES) 120 119 121
40: 218 type=116 (ANGLES) 120 119 134
40: 219 type=119 (ANGLES) 121 119 134
40: 220 type=118 (ANGLES) 119 121 122
40: 221 type=118 (ANGLES) 119 121 123
40: 222 type=120 (ANGLES) 119 121 124
40: 223 type=121 (ANGLES) 122 121 123
40: 224 type=118 (ANGLES) 122 121 124
40: 225 type=118 (ANGLES) 123 121 124
40: 226 type=118 (ANGLES) 121 124 125
40: 227 type=120 (ANGLES) 121 124 126
40: 228 type=120 (ANGLES) 121 124 130
40: 229 type=118 (ANGLES) 125 124 126
40: 230 type=118 (ANGLES) 125 124 130
40: 231 type=120 (ANGLES) 126 124 130
40: 232 type=118 (ANGLES) 124 126 127
40: 233 type=118 (ANGLES) 124 126 128
40: 234 type=118 (ANGLES) 124 126 129
40: 235 type=121 (ANGLES) 127 126 128
40: 236 type=121 (ANGLES) 127 126 129
40: 237 type=121 (ANGLES) 128 126 129
40: 238 type=118 (ANGLES) 124 130 131
40: 239 type=118 (ANGLES) 124 130 132
40: 240 type=118 (ANGLES) 124 130 133
40: 241 type=121 (ANGLES) 131 130 132
40: 242 type=121 (ANGLES) 131 130 133
40: 243 type=121 (ANGLES) 132 130 133
40: 244 type=122 (ANGLES) 119 134 135
40: 245 type=123 (ANGLES) 119 134 136
40: 246 type=124 (ANGLES) 135 134 136
40: 247 type=125 (ANGLES) 134 136 137
40: 248 type=126 (ANGLES) 134 136 138
40: 249 type=127 (ANGLES) 137 136 138
40: 250 type=116 (ANGLES) 136 138 139
40: 251 type=128 (ANGLES) 136 138 140
40: 252 type=129 (ANGLES) 136 138 144
40: 253 type=118 (ANGLES) 139 138 140
40: 254 type=116 (ANGLES) 139 138 144
40: 255 type=119 (ANGLES) 140 138 144
40: 256 type=118 (ANGLES) 138 140 141
40: 257 type=118 (ANGLES) 138 140 142
40: 258 type=118 (ANGLES) 138 140 143
40: 259 type=121 (ANGLES) 141 140 142
40: 260 type=121 (ANGLES) 141 140 143
40: 261 type=121 (ANGLES) 142 140 143
40: 262 type=122 (ANGLES) 138 144 145
40: 263 type=123 (ANGLES) 138 144 146
40: 264 type=124 (ANGLES) 145 144 146
40: 265 type=125 (ANGLES) 144 146 147
40: 266 type=126 (ANGLES) 144 146 148
40: 267 type=127 (ANGLES) 147 146 148
40: 268 type=116 (ANGLES) 146 148 149
40: 269 type=128 (ANGLES) 146 148 150
40: 270 type=129 (ANGLES) 146 148 154
40: 271 type=118 (ANGLES) 149 148 150
40: 272 type=116 (ANGLES) 149 148 154
40: 273 type=119 (ANGLES) 150 148 154
40: 274 type=118 (ANGLES) 148 150 151
40: 275 type=118 (ANGLES) 148 150 152
40: 276 type=118 (ANGLES) 148 150 153
40: 277 type=121 (ANGLES) 151 150 152
40: 278 type=121 (ANGLES) 151 150 153
40: 279 type=121 (ANGLES) 152 150 153
40: 280 type=122 (ANGLES) 148 154 155
40: G96Angle:
40: nr: 0
40: Restricted Angles:
40: nr: 0
40: Lin. Angle:
40: nr: 0
40: Bond-Cross:
40: nr: 0
40: BA-Cross:
40: nr: 0
40: U-B:
40: nr: 0
40: Quartic Angles:
40: nr: 0
40: Tab. Angles:
40: nr: 0
40: Proper Dih.:
40: nr: 145
40: iatoms:
40: 0 type=140 (PDIHS) 4 24 22 23
40: 1 type=141 (PDIHS) 22 26 24 25
40: 2 type=140 (PDIHS) 26 40 38 39
40: 3 type=141 (PDIHS) 38 42 40 41
40: 4 type=140 (PDIHS) 42 60 58 59
40: 5 type=142 (PDIHS) 44 47 50 48
40: 6 type=142 (PDIHS) 47 52 48 49
40: 7 type=142 (PDIHS) 47 54 50 51
40: 8 type=142 (PDIHS) 48 56 52 53
40: 9 type=142 (PDIHS) 50 56 54 55
40: 10 type=142 (PDIHS) 52 54 56 57
40: 11 type=141 (PDIHS) 58 62 60 61
40: 12 type=140 (PDIHS) 62 67 65 66
40: 13 type=141 (PDIHS) 65 69 67 68
40: 14 type=140 (PDIHS) 69 91 89 90
40: 15 type=141 (PDIHS) 77 82 80 81
40: 16 type=140 (PDIHS) 80 83 82 86
40: 17 type=141 (PDIHS) 82 84 83 85
40: 18 type=141 (PDIHS) 82 87 86 88
40: 19 type=141 (PDIHS) 89 93 91 92
40: 20 type=140 (PDIHS) 93 102 100 101
40: 21 type=141 (PDIHS) 100 104 102 103
40: 22 type=140 (PDIHS) 104 117 115 116
40: 23 type=140 (PDIHS) 109 113 112 114
40: 24 type=141 (PDIHS) 115 119 117 118
40: 25 type=140 (PDIHS) 119 136 134 135
40: 26 type=141 (PDIHS) 134 138 136 137
40: 27 type=140 (PDIHS) 138 146 144 145
40: 28 type=141 (PDIHS) 144 148 146 147
40: Ryckaert-Bell.:
40: nr: 1565
40: iatoms:
40: 0 type=143 (RBDIHS) 1 0 4 5
40: 1 type=144 (RBDIHS) 1 0 4 6
40: 2 type=144 (RBDIHS) 1 0 4 22
40: 3 type=143 (RBDIHS) 2 0 4 5
40: 4 type=144 (RBDIHS) 2 0 4 6
40: 5 type=144 (RBDIHS) 2 0 4 22
40: 6 type=143 (RBDIHS) 3 0 4 5
40: 7 type=144 (RBDIHS) 3 0 4 6
40: 8 type=144 (RBDIHS) 3 0 4 22
40: 9 type=145 (RBDIHS) 0 4 6 9
40: 10 type=146 (RBDIHS) 22 4 6 9
40: 11 type=147 (RBDIHS) 0 4 6 7
40: 12 type=147 (RBDIHS) 0 4 6 8
40: 13 type=148 (RBDIHS) 5 4 6 7
40: 14 type=148 (RBDIHS) 5 4 6 8
40: 15 type=148 (RBDIHS) 5 4 6 9
40: 16 type=149 (RBDIHS) 22 4 6 7
40: 17 type=149 (RBDIHS) 22 4 6 8
40: 18 type=150 (RBDIHS) 0 4 22 24
40: 19 type=151 (RBDIHS) 6 4 22 24
40: 20 type=148 (RBDIHS) 4 6 9 10
40: 21 type=148 (RBDIHS) 4 6 9 11
40: 22 type=152 (RBDIHS) 4 6 9 12
40: 23 type=148 (RBDIHS) 7 6 9 10
40: 24 type=148 (RBDIHS) 7 6 9 11
40: 25 type=148 (RBDIHS) 7 6 9 12
40: 26 type=148 (RBDIHS) 8 6 9 10
40: 27 type=148 (RBDIHS) 8 6 9 11
40: 28 type=148 (RBDIHS) 8 6 9 12
40: 29 type=148 (RBDIHS) 6 9 12 13
40: 30 type=148 (RBDIHS) 6 9 12 14
40: 31 type=152 (RBDIHS) 6 9 12 15
40: 32 type=148 (RBDIHS) 10 9 12 13
40: 33 type=148 (RBDIHS) 10 9 12 14
40: 34 type=148 (RBDIHS) 10 9 12 15
40: 35 type=148 (RBDIHS) 11 9 12 13
40: 36 type=148 (RBDIHS) 11 9 12 14
40: 37 type=148 (RBDIHS) 11 9 12 15
40: 38 type=148 (RBDIHS) 9 12 15 16
40: 39 type=148 (RBDIHS) 9 12 15 17
40: 40 type=153 (RBDIHS) 9 12 15 18
40: 41 type=148 (RBDIHS) 13 12 15 16
40: 42 type=148 (RBDIHS) 13 12 15 17
40: 43 type=154 (RBDIHS) 13 12 15 18
40: 44 type=148 (RBDIHS) 14 12 15 16
40: 45 type=148 (RBDIHS) 14 12 15 17
40: 46 type=154 (RBDIHS) 14 12 15 18
40: 47 type=144 (RBDIHS) 12 15 18 19
40: 48 type=144 (RBDIHS) 12 15 18 20
40: 49 type=144 (RBDIHS) 12 15 18 21
40: 50 type=143 (RBDIHS) 16 15 18 19
40: 51 type=143 (RBDIHS) 16 15 18 20
40: 52 type=143 (RBDIHS) 16 15 18 21
40: 53 type=143 (RBDIHS) 17 15 18 19
40: 54 type=143 (RBDIHS) 17 15 18 20
40: 55 type=143 (RBDIHS) 17 15 18 21
40: 56 type=155 (RBDIHS) 4 22 24 25
40: 57 type=156 (RBDIHS) 4 22 24 26
40: 58 type=155 (RBDIHS) 23 22 24 25
40: 59 type=157 (RBDIHS) 23 22 24 26
40: 60 type=158 (RBDIHS) 22 24 26 28
40: 61 type=159 (RBDIHS) 22 24 26 38
40: 62 type=160 (RBDIHS) 24 26 28 30
40: 63 type=160 (RBDIHS) 24 26 28 34
40: 64 type=161 (RBDIHS) 38 26 28 30
40: 65 type=161 (RBDIHS) 38 26 28 34
40: 66 type=147 (RBDIHS) 24 26 28 29
40: 67 type=148 (RBDIHS) 27 26 28 29
40: 68 type=148 (RBDIHS) 27 26 28 30
40: 69 type=148 (RBDIHS) 27 26 28 34
40: 70 type=149 (RBDIHS) 38 26 28 29
40: 71 type=150 (RBDIHS) 24 26 38 40
40: 72 type=151 (RBDIHS) 28 26 38 40
40: 73 type=148 (RBDIHS) 26 28 30 31
40: 74 type=148 (RBDIHS) 26 28 30 32
40: 75 type=148 (RBDIHS) 26 28 30 33
40: 76 type=148 (RBDIHS) 29 28 30 31
40: 77 type=148 (RBDIHS) 29 28 30 32
40: 78 type=148 (RBDIHS) 29 28 30 33
40: 79 type=148 (RBDIHS) 34 28 30 31
40: 80 type=148 (RBDIHS) 34 28 30 32
40: 81 type=148 (RBDIHS) 34 28 30 33
40: 82 type=148 (RBDIHS) 26 28 34 35
40: 83 type=148 (RBDIHS) 26 28 34 36
40: 84 type=148 (RBDIHS) 26 28 34 37
40: 85 type=148 (RBDIHS) 29 28 34 35
40: 86 type=148 (RBDIHS) 29 28 34 36
40: 87 type=148 (RBDIHS) 29 28 34 37
40: 88 type=148 (RBDIHS) 30 28 34 35
40: 89 type=148 (RBDIHS) 30 28 34 36
40: 90 type=148 (RBDIHS) 30 28 34 37
40: 91 type=155 (RBDIHS) 26 38 40 41
40: 92 type=156 (RBDIHS) 26 38 40 42
40: 93 type=155 (RBDIHS) 39 38 40 41
40: 94 type=157 (RBDIHS) 39 38 40 42
40: 95 type=158 (RBDIHS) 38 40 42 44
40: 96 type=159 (RBDIHS) 38 40 42 58
40: 97 type=147 (RBDIHS) 40 42 44 45
40: 98 type=147 (RBDIHS) 40 42 44 46
40: 99 type=162 (RBDIHS) 40 42 44 47
40: 100 type=148 (RBDIHS) 43 42 44 45
40: 101 type=148 (RBDIHS) 43 42 44 46
40: 102 type=163 (RBDIHS) 43 42 44 47
40: 103 type=149 (RBDIHS) 58 42 44 45
40: 104 type=149 (RBDIHS) 58 42 44 46
40: 105 type=164 (RBDIHS) 58 42 44 47
40: 106 type=150 (RBDIHS) 40 42 58 60
40: 107 type=151 (RBDIHS) 44 42 58 60
40: 108 type=165 (RBDIHS) 44 47 48 49
40: 109 type=165 (RBDIHS) 44 47 48 52
40: 110 type=165 (RBDIHS) 50 47 48 49
40: 111 type=165 (RBDIHS) 50 47 48 52
40: 112 type=165 (RBDIHS) 44 47 50 51
40: 113 type=165 (RBDIHS) 44 47 50 54
40: 114 type=165 (RBDIHS) 48 47 50 51
40: 115 type=165 (RBDIHS) 48 47 50 54
40: 116 type=165 (RBDIHS) 47 48 52 53
40: 117 type=165 (RBDIHS) 47 48 52 56
40: 118 type=165 (RBDIHS) 49 48 52 53
40: 119 type=165 (RBDIHS) 49 48 52 56
40: 120 type=165 (RBDIHS) 47 50 54 55
40: 121 type=165 (RBDIHS) 47 50 54 56
40: 122 type=165 (RBDIHS) 51 50 54 55
40: 123 type=165 (RBDIHS) 51 50 54 56
40: 124 type=165 (RBDIHS) 48 52 56 54
40: 125 type=165 (RBDIHS) 48 52 56 57
40: 126 type=165 (RBDIHS) 53 52 56 54
40: 127 type=165 (RBDIHS) 53 52 56 57
40: 128 type=165 (RBDIHS) 50 54 56 52
40: 129 type=165 (RBDIHS) 50 54 56 57
40: 130 type=165 (RBDIHS) 55 54 56 52
40: 131 type=165 (RBDIHS) 55 54 56 57
40: 132 type=155 (RBDIHS) 42 58 60 61
40: 133 type=156 (RBDIHS) 42 58 60 62
40: 134 type=155 (RBDIHS) 59 58 60 61
40: 135 type=157 (RBDIHS) 59 58 60 62
40: 136 type=159 (RBDIHS) 58 60 62 65
40: 137 type=150 (RBDIHS) 60 62 65 67
40: 138 type=155 (RBDIHS) 62 65 67 68
40: 139 type=156 (RBDIHS) 62 65 67 69
40: 140 type=155 (RBDIHS) 66 65 67 68
40: 141 type=157 (RBDIHS) 66 65 67 69
40: 142 type=158 (RBDIHS) 65 67 69 71
40: 143 type=159 (RBDIHS) 65 67 69 89
40: 144 type=166 (RBDIHS) 67 69 71 74
40: 145 type=167 (RBDIHS) 89 69 71 74
40: 146 type=147 (RBDIHS) 67 69 71 72
40: 147 type=147 (RBDIHS) 67 69 71 73
40: 148 type=148 (RBDIHS) 70 69 71 72
40: 149 type=148 (RBDIHS) 70 69 71 73
40: 150 type=148 (RBDIHS) 70 69 71 74
40: 151 type=149 (RBDIHS) 89 69 71 72
40: 152 type=149 (RBDIHS) 89 69 71 73
40: 153 type=150 (RBDIHS) 67 69 89 91
40: 154 type=151 (RBDIHS) 71 69 89 91
40: 155 type=148 (RBDIHS) 69 71 74 75
40: 156 type=148 (RBDIHS) 69 71 74 76
40: 157 type=152 (RBDIHS) 69 71 74 77
40: 158 type=148 (RBDIHS) 72 71 74 75
40: 159 type=148 (RBDIHS) 72 71 74 76
40: 160 type=148 (RBDIHS) 72 71 74 77
40: 161 type=148 (RBDIHS) 73 71 74 75
40: 162 type=148 (RBDIHS) 73 71 74 76
40: 163 type=148 (RBDIHS) 73 71 74 77
40: 164 type=148 (RBDIHS) 71 74 77 78
40: 165 type=148 (RBDIHS) 71 74 77 79
40: 166 type=153 (RBDIHS) 71 74 77 80
40: 167 type=148 (RBDIHS) 75 74 77 78
40: 168 type=148 (RBDIHS) 75 74 77 79
40: 169 type=168 (RBDIHS) 75 74 77 80
40: 170 type=148 (RBDIHS) 76 74 77 78
40: 171 type=148 (RBDIHS) 76 74 77 79
40: 172 type=168 (RBDIHS) 76 74 77 80
40: 173 type=169 (RBDIHS) 74 77 80 81
40: 174 type=170 (RBDIHS) 74 77 80 82
40: 175 type=171 (RBDIHS) 78 77 80 82
40: 176 type=171 (RBDIHS) 79 77 80 82
40: 177 type=172 (RBDIHS) 77 80 82 83
40: 178 type=172 (RBDIHS) 77 80 82 86
40: 179 type=173 (RBDIHS) 81 80 82 83
40: 180 type=173 (RBDIHS) 81 80 82 86
40: 181 type=173 (RBDIHS) 80 82 83 84
40: 182 type=173 (RBDIHS) 80 82 83 85
40: 183 type=173 (RBDIHS) 86 82 83 84
40: 184 type=173 (RBDIHS) 86 82 83 85
40: 185 type=173 (RBDIHS) 80 82 86 87
40: 186 type=173 (RBDIHS) 80 82 86 88
40: 187 type=173 (RBDIHS) 83 82 86 87
40: 188 type=173 (RBDIHS) 83 82 86 88
40: 189 type=155 (RBDIHS) 69 89 91 92
40: 190 type=156 (RBDIHS) 69 89 91 93
40: 191 type=155 (RBDIHS) 90 89 91 92
40: 192 type=157 (RBDIHS) 90 89 91 93
40: 193 type=158 (RBDIHS) 89 91 93 95
40: 194 type=159 (RBDIHS) 89 91 93 100
40: 195 type=174 (RBDIHS) 91 93 95 98
40: 196 type=175 (RBDIHS) 100 93 95 98
40: 197 type=147 (RBDIHS) 91 93 95 96
40: 198 type=147 (RBDIHS) 91 93 95 97
40: 199 type=148 (RBDIHS) 94 93 95 96
40: 200 type=148 (RBDIHS) 94 93 95 97
40: 201 type=176 (RBDIHS) 94 93 95 98
40: 202 type=149 (RBDIHS) 100 93 95 96
40: 203 type=149 (RBDIHS) 100 93 95 97
40: 204 type=150 (RBDIHS) 91 93 100 102
40: 205 type=151 (RBDIHS) 95 93 100 102
40: 206 type=177 (RBDIHS) 93 95 98 99
40: 207 type=178 (RBDIHS) 96 95 98 99
40: 208 type=178 (RBDIHS) 97 95 98 99
40: 209 type=155 (RBDIHS) 93 100 102 103
40: 210 type=156 (RBDIHS) 93 100 102 104
40: 211 type=155 (RBDIHS) 101 100 102 103
40: 212 type=157 (RBDIHS) 101 100 102 104
40: 213 type=158 (RBDIHS) 100 102 104 106
40: 214 type=159 (RBDIHS) 100 102 104 115
40: 215 type=179 (RBDIHS) 102 104 106 109
40: 216 type=180 (RBDIHS) 115 104 106 109
40: 217 type=147 (RBDIHS) 102 104 106 107
40: 218 type=147 (RBDIHS) 102 104 106 108
40: 219 type=148 (RBDIHS) 105 104 106 107
40: 220 type=148 (RBDIHS) 105 104 106 108
40: 221 type=148 (RBDIHS) 105 104 106 109
40: 222 type=149 (RBDIHS) 115 104 106 107
40: 223 type=149 (RBDIHS) 115 104 106 108
40: 224 type=150 (RBDIHS) 102 104 115 117
40: 225 type=151 (RBDIHS) 106 104 115 117
40: 226 type=148 (RBDIHS) 104 106 109 110
40: 227 type=148 (RBDIHS) 104 106 109 111
40: 228 type=181 (RBDIHS) 104 106 109 112
40: 229 type=148 (RBDIHS) 107 106 109 110
40: 230 type=148 (RBDIHS) 107 106 109 111
40: 231 type=182 (RBDIHS) 107 106 109 112
40: 232 type=148 (RBDIHS) 108 106 109 110
40: 233 type=148 (RBDIHS) 108 106 109 111
40: 234 type=182 (RBDIHS) 108 106 109 112
40: 235 type=183 (RBDIHS) 106 109 112 113
40: 236 type=183 (RBDIHS) 106 109 112 114
40: 237 type=155 (RBDIHS) 104 115 117 118
40: 238 type=156 (RBDIHS) 104 115 117 119
40: 239 type=155 (RBDIHS) 116 115 117 118
40: 240 type=157 (RBDIHS) 116 115 117 119
40: 241 type=158 (RBDIHS) 115 117 119 121
40: 242 type=159 (RBDIHS) 115 117 119 134
40: 243 type=184 (RBDIHS) 117 119 121 124
40: 244 type=185 (RBDIHS) 134 119 121 124
40: 245 type=147 (RBDIHS) 117 119 121 122
40: 246 type=147 (RBDIHS) 117 119 121 123
40: 247 type=148 (RBDIHS) 120 119 121 122
40: 248 type=148 (RBDIHS) 120 119 121 123
40: 249 type=148 (RBDIHS) 120 119 121 124
40: 250 type=149 (RBDIHS) 134 119 121 122
40: 251 type=149 (RBDIHS) 134 119 121 123
40: 252 type=150 (RBDIHS) 117 119 134 136
40: 253 type=151 (RBDIHS) 121 119 134 136
40: 254 type=148 (RBDIHS) 119 121 124 125
40: 255 type=152 (RBDIHS) 119 121 124 126
40: 256 type=152 (RBDIHS) 119 121 124 130
40: 257 type=148 (RBDIHS) 122 121 124 125
40: 258 type=148 (RBDIHS) 122 121 124 126
40: 259 type=148 (RBDIHS) 122 121 124 130
40: 260 type=148 (RBDIHS) 123 121 124 125
40: 261 type=148 (RBDIHS) 123 121 124 126
40: 262 type=148 (RBDIHS) 123 121 124 130
40: 263 type=148 (RBDIHS) 121 124 126 127
40: 264 type=148 (RBDIHS) 121 124 126 128
40: 265 type=148 (RBDIHS) 121 124 126 129
40: 266 type=148 (RBDIHS) 125 124 126 127
40: 267 type=148 (RBDIHS) 125 124 126 128
40: 268 type=148 (RBDIHS) 125 124 126 129
40: 269 type=148 (RBDIHS) 130 124 126 127
40: 270 type=148 (RBDIHS) 130 124 126 128
40: 271 type=148 (RBDIHS) 130 124 126 129
40: 272 type=148 (RBDIHS) 121 124 130 131
40: 273 type=148 (RBDIHS) 121 124 130 132
40: 274 type=148 (RBDIHS) 121 124 130 133
40: 275 type=148 (RBDIHS) 125 124 130 131
40: 276 type=148 (RBDIHS) 125 124 130 132
40: 277 type=148 (RBDIHS) 125 124 130 133
40: 278 type=148 (RBDIHS) 126 124 130 131
40: 279 type=148 (RBDIHS) 126 124 130 132
40: 280 type=148 (RBDIHS) 126 124 130 133
40: 281 type=155 (RBDIHS) 119 134 136 137
40: 282 type=156 (RBDIHS) 119 134 136 138
40: 283 type=155 (RBDIHS) 135 134 136 137
40: 284 type=157 (RBDIHS) 135 134 136 138
40: 285 type=158 (RBDIHS) 134 136 138 140
40: 286 type=159 (RBDIHS) 134 136 138 144
40: 287 type=147 (RBDIHS) 136 138 140 141
40: 288 type=147 (RBDIHS) 136 138 140 142
40: 289 type=147 (RBDIHS) 136 138 140 143
40: 290 type=148 (RBDIHS) 139 138 140 141
40: 291 type=148 (RBDIHS) 139 138 140 142
40: 292 type=148 (RBDIHS) 139 138 140 143
40: 293 type=149 (RBDIHS) 144 138 140 141
40: 294 type=149 (RBDIHS) 144 138 140 142
40: 295 type=149 (RBDIHS) 144 138 140 143
40: 296 type=150 (RBDIHS) 136 138 144 146
40: 297 type=151 (RBDIHS) 140 138 144 146
40: 298 type=155 (RBDIHS) 138 144 146 147
40: 299 type=156 (RBDIHS) 138 144 146 148
40: 300 type=155 (RBDIHS) 145 144 146 147
40: 301 type=157 (RBDIHS) 145 144 146 148
40: 302 type=158 (RBDIHS) 144 146 148 150
40: 303 type=159 (RBDIHS) 144 146 148 154
40: 304 type=147 (RBDIHS) 146 148 150 151
40: 305 type=147 (RBDIHS) 146 148 150 152
40: 306 type=147 (RBDIHS) 146 148 150 153
40: 307 type=148 (RBDIHS) 149 148 150 151
40: 308 type=148 (RBDIHS) 149 148 150 152
40: 309 type=148 (RBDIHS) 149 148 150 153
40: 310 type=149 (RBDIHS) 154 148 150 151
40: 311 type=149 (RBDIHS) 154 148 150 152
40: 312 type=149 (RBDIHS) 154 148 150 153
40: Restricted Dih.:
40: nr: 0
40: CBT Dih.:
40: nr: 0
40: Fourier Dih.:
40: nr: 0
40: Improper Dih.:
40: nr: 0
40: Improper Dih.:
40: nr: 0
40: Tab. Dih.:
40: nr: 0
40: CMAP Dih.:
40: nr: 0
40: GB 1-2 Pol. (unused):
40: nr: 0
40: GB 1-3 Pol. (unused):
40: nr: 0
40: GB 1-4 Pol. (unused):
40: nr: 0
40: GB Polarization (unused):
40: nr: 0
40: Nonpolar Sol. (unused):
40: nr: 0
40: LJ-14:
40: nr: 1197
40: iatoms:
40: 0 type=186 (LJ14) 0 7
40: 1 type=186 (LJ14) 0 8
40: 2 type=187 (LJ14) 0 9
40: 3 type=188 (LJ14) 0 23
40: 4 type=189 (LJ14) 0 24
40: 5 type=190 (LJ14) 1 5
40: 6 type=190 (LJ14) 1 6
40: 7 type=190 (LJ14) 1 22
40: 8 type=190 (LJ14) 2 5
40: 9 type=190 (LJ14) 2 6
40: 10 type=190 (LJ14) 2 22
40: 11 type=190 (LJ14) 3 5
40: 12 type=190 (LJ14) 3 6
40: 13 type=190 (LJ14) 3 22
40: 14 type=191 (LJ14) 4 10
40: 15 type=191 (LJ14) 4 11
40: 16 type=192 (LJ14) 4 12
40: 17 type=190 (LJ14) 4 25
40: 18 type=192 (LJ14) 4 26
40: 19 type=193 (LJ14) 5 7
40: 20 type=193 (LJ14) 5 8
40: 21 type=191 (LJ14) 5 9
40: 22 type=194 (LJ14) 5 23
40: 23 type=186 (LJ14) 5 24
40: 24 type=191 (LJ14) 6 13
40: 25 type=191 (LJ14) 6 14
40: 26 type=192 (LJ14) 6 15
40: 27 type=195 (LJ14) 6 23
40: 28 type=187 (LJ14) 6 24
40: 29 type=193 (LJ14) 7 10
40: 30 type=193 (LJ14) 7 11
40: 31 type=191 (LJ14) 7 12
40: 32 type=196 (LJ14) 7 22
40: 33 type=193 (LJ14) 8 10
40: 34 type=193 (LJ14) 8 11
40: 35 type=191 (LJ14) 8 12
40: 36 type=196 (LJ14) 8 22
40: 37 type=191 (LJ14) 9 16
40: 38 type=191 (LJ14) 9 17
40: 39 type=187 (LJ14) 9 18
40: 40 type=197 (LJ14) 9 22
40: 41 type=193 (LJ14) 10 13
40: 42 type=193 (LJ14) 10 14
40: 43 type=191 (LJ14) 10 15
40: 44 type=193 (LJ14) 11 13
40: 45 type=193 (LJ14) 11 14
40: 46 type=191 (LJ14) 11 15
40: 47 type=190 (LJ14) 12 19
40: 48 type=190 (LJ14) 12 20
40: 49 type=190 (LJ14) 12 21
40: 50 type=193 (LJ14) 13 16
40: 51 type=193 (LJ14) 13 17
40: 52 type=186 (LJ14) 13 18
40: 53 type=193 (LJ14) 14 16
40: 54 type=193 (LJ14) 14 17
40: 55 type=186 (LJ14) 14 18
40: 56 type=190 (LJ14) 16 19
40: 57 type=190 (LJ14) 16 20
40: 58 type=190 (LJ14) 16 21
40: 59 type=190 (LJ14) 17 19
40: 60 type=190 (LJ14) 17 20
40: 61 type=190 (LJ14) 17 21
40: 62 type=196 (LJ14) 22 27
40: 63 type=197 (LJ14) 22 28
40: 64 type=198 (LJ14) 22 38
40: 65 type=190 (LJ14) 23 25
40: 66 type=195 (LJ14) 23 26
40: 67 type=186 (LJ14) 24 29
40: 68 type=187 (LJ14) 24 30
40: 69 type=187 (LJ14) 24 34
40: 70 type=188 (LJ14) 24 39
40: 71 type=189 (LJ14) 24 40
40: 72 type=190 (LJ14) 25 27
40: 73 type=190 (LJ14) 25 28
40: 74 type=190 (LJ14) 25 38
40: 75 type=191 (LJ14) 26 31
40: 76 type=191 (LJ14) 26 32
40: 77 type=191 (LJ14) 26 33
40: 78 type=191 (LJ14) 26 35
40: 79 type=191 (LJ14) 26 36
40: 80 type=191 (LJ14) 26 37
40: 81 type=190 (LJ14) 26 41
40: 82 type=192 (LJ14) 26 42
40: 83 type=193 (LJ14) 27 29
40: 84 type=191 (LJ14) 27 30
40: 85 type=191 (LJ14) 27 34
40: 86 type=194 (LJ14) 27 39
40: 87 type=186 (LJ14) 27 40
40: 88 type=195 (LJ14) 28 39
40: 89 type=187 (LJ14) 28 40
40: 90 type=193 (LJ14) 29 31
40: 91 type=193 (LJ14) 29 32
40: 92 type=193 (LJ14) 29 33
40: 93 type=193 (LJ14) 29 35
40: 94 type=193 (LJ14) 29 36
40: 95 type=193 (LJ14) 29 37
40: 96 type=196 (LJ14) 29 38
40: 97 type=191 (LJ14) 30 35
40: 98 type=191 (LJ14) 30 36
40: 99 type=191 (LJ14) 30 37
40: 100 type=197 (LJ14) 30 38
40: 101 type=191 (LJ14) 31 34
40: 102 type=191 (LJ14) 32 34
40: 103 type=191 (LJ14) 33 34
40: 104 type=197 (LJ14) 34 38
40: 105 type=196 (LJ14) 38 43
40: 106 type=197 (LJ14) 38 44
40: 107 type=198 (LJ14) 38 58
40: 108 type=190 (LJ14) 39 41
40: 109 type=195 (LJ14) 39 42
40: 110 type=186 (LJ14) 40 45
40: 111 type=186 (LJ14) 40 46
40: 112 type=199 (LJ14) 40 47
40: 113 type=188 (LJ14) 40 59
40: 114 type=189 (LJ14) 40 60
40: 115 type=190 (LJ14) 41 43
40: 116 type=190 (LJ14) 41 44
40: 117 type=190 (LJ14) 41 58
40: 118 type=200 (LJ14) 42 48
40: 119 type=200 (LJ14) 42 50
40: 120 type=190 (LJ14) 42 61
40: 121 type=192 (LJ14) 42 62
40: 122 type=193 (LJ14) 43 45
40: 123 type=193 (LJ14) 43 46
40: 124 type=201 (LJ14) 43 47
40: 125 type=194 (LJ14) 43 59
40: 126 type=186 (LJ14) 43 60
40: 127 type=202 (LJ14) 44 49
40: 128 type=202 (LJ14) 44 51
40: 129 type=200 (LJ14) 44 52
40: 130 type=200 (LJ14) 44 54
40: 131 type=195 (LJ14) 44 59
40: 132 type=187 (LJ14) 44 60
40: 133 type=201 (LJ14) 45 48
40: 134 type=201 (LJ14) 45 50
40: 135 type=196 (LJ14) 45 58
40: 136 type=201 (LJ14) 46 48
40: 137 type=201 (LJ14) 46 50
40: 138 type=196 (LJ14) 46 58
40: 139 type=203 (LJ14) 47 53
40: 140 type=203 (LJ14) 47 55
40: 141 type=204 (LJ14) 47 56
40: 142 type=205 (LJ14) 47 58
40: 143 type=203 (LJ14) 48 51
40: 144 type=204 (LJ14) 48 54
40: 145 type=203 (LJ14) 48 57
40: 146 type=203 (LJ14) 49 50
40: 147 type=206 (LJ14) 49 53
40: 148 type=203 (LJ14) 49 56
40: 149 type=204 (LJ14) 50 52
40: 150 type=203 (LJ14) 50 57
40: 151 type=206 (LJ14) 51 55
40: 152 type=203 (LJ14) 51 56
40: 153 type=203 (LJ14) 52 55
40: 154 type=203 (LJ14) 53 54
40: 155 type=206 (LJ14) 53 57
40: 156 type=206 (LJ14) 55 57
40: 157 type=196 (LJ14) 58 63
40: 158 type=196 (LJ14) 58 64
40: 159 type=198 (LJ14) 58 65
40: 160 type=190 (LJ14) 59 61
40: 161 type=195 (LJ14) 59 62
40: 162 type=188 (LJ14) 60 66
40: 163 type=189 (LJ14) 60 67
40: 164 type=190 (LJ14) 61 63
40: 165 type=190 (LJ14) 61 64
40: 166 type=190 (LJ14) 61 65
40: 167 type=190 (LJ14) 62 68
40: 168 type=192 (LJ14) 62 69
40: 169 type=194 (LJ14) 63 66
40: 170 type=186 (LJ14) 63 67
40: 171 type=194 (LJ14) 64 66
40: 172 type=186 (LJ14) 64 67
40: 173 type=196 (LJ14) 65 70
40: 174 type=197 (LJ14) 65 71
40: 175 type=198 (LJ14) 65 89
40: 176 type=190 (LJ14) 66 68
40: 177 type=195 (LJ14) 66 69
40: 178 type=186 (LJ14) 67 72
40: 179 type=186 (LJ14) 67 73
40: 180 type=187 (LJ14) 67 74
40: 181 type=188 (LJ14) 67 90
40: 182 type=189 (LJ14) 67 91
40: 183 type=190 (LJ14) 68 70
40: 184 type=190 (LJ14) 68 71
40: 185 type=190 (LJ14) 68 89
40: 186 type=191 (LJ14) 69 75
40: 187 type=191 (LJ14) 69 76
40: 188 type=192 (LJ14) 69 77
40: 189 type=190 (LJ14) 69 92
40: 190 type=192 (LJ14) 69 93
40: 191 type=193 (LJ14) 70 72
40: 192 type=193 (LJ14) 70 73
40: 193 type=191 (LJ14) 70 74
40: 194 type=194 (LJ14) 70 90
40: 195 type=186 (LJ14) 70 91
40: 196 type=191 (LJ14) 71 78
40: 197 type=191 (LJ14) 71 79
40: 198 type=187 (LJ14) 71 80
40: 199 type=195 (LJ14) 71 90
40: 200 type=187 (LJ14) 71 91
40: 201 type=193 (LJ14) 72 75
40: 202 type=193 (LJ14) 72 76
40: 203 type=191 (LJ14) 72 77
40: 204 type=196 (LJ14) 72 89
40: 205 type=193 (LJ14) 73 75
40: 206 type=193 (LJ14) 73 76
40: 207 type=191 (LJ14) 73 77
40: 208 type=196 (LJ14) 73 89
40: 209 type=190 (LJ14) 74 81
40: 210 type=207 (LJ14) 74 82
40: 211 type=197 (LJ14) 74 89
40: 212 type=193 (LJ14) 75 78
40: 213 type=193 (LJ14) 75 79
40: 214 type=186 (LJ14) 75 80
40: 215 type=193 (LJ14) 76 78
40: 216 type=193 (LJ14) 76 79
40: 217 type=186 (LJ14) 76 80
40: 218 type=187 (LJ14) 77 83
40: 219 type=187 (LJ14) 77 86
40: 220 type=190 (LJ14) 78 81
40: 221 type=208 (LJ14) 78 82
40: 222 type=190 (LJ14) 79 81
40: 223 type=208 (LJ14) 79 82
40: 224 type=190 (LJ14) 80 84
40: 225 type=190 (LJ14) 80 85
40: 226 type=190 (LJ14) 80 87
40: 227 type=190 (LJ14) 80 88
40: 228 type=190 (LJ14) 81 83
40: 229 type=190 (LJ14) 81 86
40: 230 type=190 (LJ14) 83 87
40: 231 type=190 (LJ14) 83 88
40: 232 type=190 (LJ14) 84 86
40: 233 type=190 (LJ14) 85 86
40: 234 type=196 (LJ14) 89 94
40: 235 type=197 (LJ14) 89 95
40: 236 type=198 (LJ14) 89 100
40: 237 type=190 (LJ14) 90 92
40: 238 type=195 (LJ14) 90 93
40: 239 type=186 (LJ14) 91 96
40: 240 type=186 (LJ14) 91 97
40: 241 type=209 (LJ14) 91 98
40: 242 type=188 (LJ14) 91 101
40: 243 type=189 (LJ14) 91 102
40: 244 type=190 (LJ14) 92 94
40: 245 type=190 (LJ14) 92 95
40: 246 type=190 (LJ14) 92 100
40: 247 type=190 (LJ14) 93 99
40: 248 type=190 (LJ14) 93 103
40: 249 type=192 (LJ14) 93 104
40: 250 type=193 (LJ14) 94 96
40: 251 type=193 (LJ14) 94 97
40: 252 type=210 (LJ14) 94 98
40: 253 type=194 (LJ14) 94 101
40: 254 type=186 (LJ14) 94 102
40: 255 type=195 (LJ14) 95 101
40: 256 type=187 (LJ14) 95 102
40: 257 type=190 (LJ14) 96 99
40: 258 type=196 (LJ14) 96 100
40: 259 type=190 (LJ14) 97 99
40: 260 type=196 (LJ14) 97 100
40: 261 type=211 (LJ14) 98 100
40: 262 type=196 (LJ14) 100 105
40: 263 type=197 (LJ14) 100 106
40: 264 type=198 (LJ14) 100 115
40: 265 type=190 (LJ14) 101 103
40: 266 type=195 (LJ14) 101 104
40: 267 type=186 (LJ14) 102 107
40: 268 type=186 (LJ14) 102 108
40: 269 type=187 (LJ14) 102 109
40: 270 type=188 (LJ14) 102 116
40: 271 type=189 (LJ14) 102 117
40: 272 type=190 (LJ14) 103 105
40: 273 type=190 (LJ14) 103 106
40: 274 type=190 (LJ14) 103 115
40: 275 type=191 (LJ14) 104 110
40: 276 type=191 (LJ14) 104 111
40: 277 type=197 (LJ14) 104 112
40: 278 type=190 (LJ14) 104 118
40: 279 type=192 (LJ14) 104 119
40: 280 type=193 (LJ14) 105 107
40: 281 type=193 (LJ14) 105 108
40: 282 type=191 (LJ14) 105 109
40: 283 type=194 (LJ14) 105 116
40: 284 type=186 (LJ14) 105 117
40: 285 type=195 (LJ14) 106 113
40: 286 type=195 (LJ14) 106 114
40: 287 type=195 (LJ14) 106 116
40: 288 type=187 (LJ14) 106 117
40: 289 type=193 (LJ14) 107 110
40: 290 type=193 (LJ14) 107 111
40: 291 type=196 (LJ14) 107 112
40: 292 type=196 (LJ14) 107 115
40: 293 type=193 (LJ14) 108 110
40: 294 type=193 (LJ14) 108 111
40: 295 type=196 (LJ14) 108 112
40: 296 type=196 (LJ14) 108 115
40: 297 type=197 (LJ14) 109 115
40: 298 type=194 (LJ14) 110 113
40: 299 type=194 (LJ14) 110 114
40: 300 type=194 (LJ14) 111 113
40: 301 type=194 (LJ14) 111 114
40: 302 type=196 (LJ14) 115 120
40: 303 type=197 (LJ14) 115 121
40: 304 type=198 (LJ14) 115 134
40: 305 type=190 (LJ14) 116 118
40: 306 type=195 (LJ14) 116 119
40: 307 type=186 (LJ14) 117 122
40: 308 type=186 (LJ14) 117 123
40: 309 type=187 (LJ14) 117 124
40: 310 type=188 (LJ14) 117 135
40: 311 type=189 (LJ14) 117 136
40: 312 type=190 (LJ14) 118 120
40: 313 type=190 (LJ14) 118 121
40: 314 type=190 (LJ14) 118 134
40: 315 type=191 (LJ14) 119 125
40: 316 type=192 (LJ14) 119 126
40: 317 type=192 (LJ14) 119 130
40: 318 type=190 (LJ14) 119 137
40: 319 type=192 (LJ14) 119 138
40: 320 type=193 (LJ14) 120 122
40: 321 type=193 (LJ14) 120 123
40: 322 type=191 (LJ14) 120 124
40: 323 type=194 (LJ14) 120 135
40: 324 type=186 (LJ14) 120 136
40: 325 type=191 (LJ14) 121 127
40: 326 type=191 (LJ14) 121 128
40: 327 type=191 (LJ14) 121 129
40: 328 type=191 (LJ14) 121 131
40: 329 type=191 (LJ14) 121 132
40: 330 type=191 (LJ14) 121 133
40: 331 type=195 (LJ14) 121 135
40: 332 type=187 (LJ14) 121 136
40: 333 type=193 (LJ14) 122 125
40: 334 type=191 (LJ14) 122 126
40: 335 type=191 (LJ14) 122 130
40: 336 type=196 (LJ14) 122 134
40: 337 type=193 (LJ14) 123 125
40: 338 type=191 (LJ14) 123 126
40: 339 type=191 (LJ14) 123 130
40: 340 type=196 (LJ14) 123 134
40: 341 type=197 (LJ14) 124 134
40: 342 type=193 (LJ14) 125 127
40: 343 type=193 (LJ14) 125 128
40: 344 type=193 (LJ14) 125 129
40: 345 type=193 (LJ14) 125 131
40: 346 type=193 (LJ14) 125 132
40: 347 type=193 (LJ14) 125 133
40: 348 type=191 (LJ14) 126 131
40: 349 type=191 (LJ14) 126 132
40: 350 type=191 (LJ14) 126 133
40: 351 type=191 (LJ14) 127 130
40: 352 type=191 (LJ14) 128 130
40: 353 type=191 (LJ14) 129 130
40: 354 type=196 (LJ14) 134 139
40: 355 type=197 (LJ14) 134 140
40: 356 type=198 (LJ14) 134 144
40: 357 type=190 (LJ14) 135 137
40: 358 type=195 (LJ14) 135 138
40: 359 type=186 (LJ14) 136 141
40: 360 type=186 (LJ14) 136 142
40: 361 type=186 (LJ14) 136 143
40: 362 type=188 (LJ14) 136 145
40: 363 type=189 (LJ14) 136 146
40: 364 type=190 (LJ14) 137 139
40: 365 type=190 (LJ14) 137 140
40: 366 type=190 (LJ14) 137 144
40: 367 type=190 (LJ14) 138 147
40: 368 type=192 (LJ14) 138 148
40: 369 type=193 (LJ14) 139 141
40: 370 type=193 (LJ14) 139 142
40: 371 type=193 (LJ14) 139 143
40: 372 type=194 (LJ14) 139 145
40: 373 type=186 (LJ14) 139 146
40: 374 type=195 (LJ14) 140 145
40: 375 type=187 (LJ14) 140 146
40: 376 type=196 (LJ14) 141 144
40: 377 type=196 (LJ14) 142 144
40: 378 type=196 (LJ14) 143 144
40: 379 type=196 (LJ14) 144 149
40: 380 type=197 (LJ14) 144 150
40: 381 type=198 (LJ14) 144 154
40: 382 type=190 (LJ14) 145 147
40: 383 type=195 (LJ14) 145 148
40: 384 type=186 (LJ14) 146 151
40: 385 type=186 (LJ14) 146 152
40: 386 type=186 (LJ14) 146 153
40: 387 type=188 (LJ14) 146 155
40: 388 type=190 (LJ14) 147 149
40: 389 type=190 (LJ14) 147 150
40: 390 type=190 (LJ14) 147 154
40: 391 type=193 (LJ14) 149 151
40: 392 type=193 (LJ14) 149 152
40: 393 type=193 (LJ14) 149 153
40: 394 type=194 (LJ14) 149 155
40: 395 type=195 (LJ14) 150 155
40: 396 type=196 (LJ14) 151 154
40: 397 type=196 (LJ14) 152 154
40: 398 type=196 (LJ14) 153 154
40: Coulomb-14:
40: nr: 0
40: LJC-14 q:
40: nr: 0
40: LJC Pairs NB:
40: nr: 0
40: LJ (SR):
40: nr: 0
40: Buck.ham (SR):
40: nr: 0
40: LJ (unused):
40: nr: 0
40: B.ham (unused):
40: nr: 0
40: Disper. corr.:
40: nr: 0
40: Coulomb (SR):
40: nr: 0
40: Coul (unused):
40: nr: 0
40: RF excl.:
40: nr: 0
40: Coul. recip.:
40: nr: 0
40: LJ recip.:
40: nr: 0
40: DPD:
40: nr: 0
40: Polarization:
40: nr: 0
40: Water Pol.:
40: nr: 0
40: Thole Pol.:
40: nr: 0
40: Anharm. Pol.:
40: nr: 0
40: Position Rest.:
40: nr: 0
40: Flat-bottom posres:
40: nr: 0
40: Dis. Rest.:
40: nr: 0
40: D.R.Viol. (nm):
40: nr: 0
40: Orient. Rest.:
40: nr: 0
40: Ori. R. RMSD:
40: nr: 0
40: Angle Rest.:
40: nr: 0
40: Angle Rest. Z:
40: nr: 0
40: Dih. Rest.:
40: nr: 0
40: Dih. Rest. Viol.:
40: nr: 0
40: Constraint:
40: nr: 0
40: Constr. No Conn.:
40: nr: 0
40: Settle:
40: nr: 0
40: Virtual site 2:
40: nr: 0
40: Virtual site 2fd:
40: nr: 0
40: Virtual site 3:
40: nr: 0
40: Virtual site 3fd:
40: nr: 0
40: Virtual site 3fad:
40: nr: 0
40: Virtual site 3out:
40: nr: 0
40: Virtual site 4fd:
40: nr: 0
40: Virtual site 4fdn:
40: nr: 0
40: Virtual site N:
40: nr: 0
40: COM Pull En.:
40: nr: 0
40: Density fitting:
40: nr: 0
40: Quantum En.:
40: nr: 0
40: Potential:
40: nr: 0
40: Kinetic En.:
40: nr: 0
40: Total Energy:
40: nr: 0
40: Conserved En.:
40: nr: 0
40: Temperature:
40: nr: 0
40: Vir. Temp. (not used):
40: nr: 0
40: Pres. DC:
40: nr: 0
40: Pressure:
40: nr: 0
40: dH/dl constr.:
40: nr: 0
40: dVremain/dl:
40: nr: 0
40: dEkin/dl:
40: nr: 0
40: dVcoul/dl:
40: nr: 0
40: dVvdw/dl:
40: nr: 0
40: dVbonded/dl:
40: nr: 0
40: dVrestraint/dl:
40: nr: 0
40: dVtemperature/dl:
40: nr: 0
40: grp[T-Coupling ] nr=1, name=[ rest]
40: grp[Energy Mon. ] nr=1, name=[ rest]
40: grp[Acceleration] nr=1, name=[ rest]
40: grp[Freeze ] nr=1, name=[ rest]
40: grp[User1 ] nr=1, name=[ rest]
40: grp[User2 ] nr=1, name=[ rest]
40: grp[VCM ] nr=1, name=[ rest]
40: grp[Compressed X] nr=1, name=[ rest]
40: grp[Or. Res. Fit] nr=1, name=[ rest]
40: grp[QMMM ] nr=1, name=[ rest]
40: grpname (11):
40: grpname[0]={name="System"}
40: grpname[1]={name="Protein"}
40: grpname[2]={name="Protein-H"}
40: grpname[3]={name="C-alpha"}
40: grpname[4]={name="Backbone"}
40: grpname[5]={name="MainChain"}
40: grpname[6]={name="MainChain+Cb"}
40: grpname[7]={name="MainChain+H"}
40: grpname[8]={name="SideChain"}
40: grpname[9]={name="SideChain-H"}
40: grpname[10]={name="rest"}
40: groups T-Cou Energ Accel Freez User1 User2 VCM Compr Or. R QMMM
40: allocated 0 0 0 0 0 0 0 0 0 0
40: groupnr[ *] = 0 0 0 0 0 0 0 0 0 0
40: box (3x3):
40: box[ 0]={ 5.90620e+00, 0.00000e+00, 0.00000e+00}
40: box[ 1]={ 0.00000e+00, 6.84510e+00, 0.00000e+00}
40: box[ 2]={ 0.00000e+00, 0.00000e+00, 3.05170e+00}
40: box_rel (3x3):
40: box_rel[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: box_rel[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: box_rel[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: boxv (3x3):
40: boxv[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: boxv[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: boxv[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: pres_prev (3x3):
40: pres_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: pres_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: pres_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: svir_prev (3x3):
40: svir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: svir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: svir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: fvir_prev (3x3):
40: fvir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: fvir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: fvir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: nosehoover_xi: not available
40: x (156x3):
40: x[ 0]={ 3.53600e+00, 2.23400e+00, -1.19800e+00}
40: x[ 1]={ 3.61200e+00, 2.28800e+00, -1.23600e+00}
40: x[ 2]={ 3.47000e+00, 2.21400e+00, -1.27000e+00}
40: x[ 3]={ 3.49200e+00, 2.28600e+00, -1.12500e+00}
40: x[ 4]={ 3.58900e+00, 2.10700e+00, -1.14300e+00}
40: x[ 5]={ 3.63300e+00, 2.05500e+00, -1.21600e+00}
40: x[ 6]={ 3.68700e+00, 2.14400e+00, -1.03100e+00}
40: x[ 7]={ 3.76300e+00, 2.19500e+00, -1.07000e+00}
40: x[ 8]={ 3.63900e+00, 2.20100e+00, -9.64000e-01}
40: x[ 9]={ 3.74500e+00, 2.02500e+00, -9.56000e-01}
40: x[ 10]={ 3.67600e+00, 1.98900e+00, -8.94000e-01}
40: x[ 11]={ 3.77000e+00, 1.95400e+00, -1.02300e+00}
40: x[ 12]={ 3.86900e+00, 2.06500e+00, -8.77000e-01}
40: x[ 13]={ 3.94500e+00, 2.08300e+00, -9.40000e-01}
40: x[ 14]={ 3.84900e+00, 2.14700e+00, -8.24000e-01}
40: x[ 15]={ 3.90600e+00, 1.95100e+00, -7.84000e-01}
40: x[ 16]={ 3.84100e+00, 1.94600e+00, -7.08000e-01}
40: x[ 17]={ 3.90600e+00, 1.86400e+00, -8.33000e-01}
40: x[ 18]={ 4.04200e+00, 1.97700e+00, -7.30000e-01}
40: x[ 19]={ 4.06900e+00, 1.90300e+00, -6.68000e-01}
40: x[ 20]={ 4.10800e+00, 1.98200e+00, -8.06000e-01}
40: x[ 21]={ 4.04200e+00, 2.06400e+00, -6.80000e-01}
40: x[ 22]={ 3.47400e+00, 2.02600e+00, -1.08400e+00}
40: x[ 23]={ 3.39500e+00, 2.08100e+00, -1.00800e+00}
40: x[ 24]={ 3.47400e+00, 1.89600e+00, -1.10400e+00}
40: x[ 25]={ 3.53600e+00, 1.86000e+00, -1.17400e+00}
40: x[ 26]={ 3.39000e+00, 1.80000e+00, -1.03300e+00}
40: x[ 27]={ 3.31700e+00, 1.85200e+00, -9.90000e-01}
40: x[ 28]={ 3.31400e+00, 1.70300e+00, -1.12300e+00}
40: x[ 29]={ 3.38600e+00, 1.65200e+00, -1.17000e+00}
40: x[ 30]={ 3.22500e+00, 1.60800e+00, -1.04300e+00}
40: x[ 31]={ 3.17700e+00, 1.54700e+00, -1.10600e+00}
40: x[ 32]={ 3.28200e+00, 1.55500e+00, -9.81000e-01}
40: x[ 33]={ 3.15800e+00, 1.66100e+00, -9.91000e-01}
40: x[ 34]={ 3.22900e+00, 1.77100e+00, -1.22900e+00}
40: x[ 35]={ 3.18300e+00, 1.70200e+00, -1.28400e+00}
40: x[ 36]={ 3.16200e+00, 1.83000e+00, -1.18500e+00}
40: x[ 37]={ 3.28800e+00, 1.82700e+00, -1.28800e+00}
40: x[ 38]={ 3.48000e+00, 1.73100e+00, -9.29000e-01}
40: x[ 39]={ 3.57600e+00, 1.66100e+00, -9.66000e-01}
40: x[ 40]={ 3.44900e+00, 1.75500e+00, -8.04000e-01}
40: x[ 41]={ 3.37500e+00, 1.81900e+00, -7.84000e-01}
40: x[ 42]={ 3.51900e+00, 1.69000e+00, -6.92000e-01}
40: x[ 43]={ 3.61500e+00, 1.69700e+00, -7.17000e-01}
40: x[ 44]={ 3.49700e+00, 1.76300e+00, -5.59000e-01}
40: x[ 45]={ 3.40500e+00, 1.80200e+00, -5.58000e-01}
40: x[ 46]={ 3.50600e+00, 1.69800e+00, -4.84000e-01}
40: x[ 47]={ 3.59400e+00, 1.87400e+00, -5.38000e-01}
40: x[ 48]={ 3.56700e+00, 2.00500e+00, -5.80000e-01}
40: x[ 49]={ 3.48100e+00, 2.02500e+00, -6.27000e-01}
40: x[ 50]={ 3.70000e+00, 1.85600e+00, -4.47000e-01}
40: x[ 51]={ 3.71300e+00, 1.76600e+00, -4.05000e-01}
40: x[ 52]={ 3.65800e+00, 2.10800e+00, -5.57000e-01}
40: x[ 53]={ 3.64800e+00, 2.19500e+00, -6.04000e-01}
40: x[ 54]={ 3.78700e+00, 1.95900e+00, -4.16000e-01}
40: x[ 55]={ 3.86600e+00, 1.94200e+00, -3.57000e-01}
40: x[ 56]={ 3.76400e+00, 2.08700e+00, -4.67000e-01}
40: x[ 57]={ 3.82200e+00, 2.16400e+00, -4.39000e-01}
40: x[ 58]={ 3.47400e+00, 1.54400e+00, -6.77000e-01}
40: x[ 59]={ 3.35200e+00, 1.51600e+00, -6.86000e-01}
40: x[ 60]={ 3.57200e+00, 1.46400e+00, -6.33000e-01}
40: x[ 61]={ 3.66700e+00, 1.49500e+00, -6.32000e-01}
40: x[ 62]={ 3.53700e+00, 1.32800e+00, -5.87000e-01}
40: x[ 63]={ 3.46200e+00, 1.29200e+00, -6.43000e-01}
40: x[ 64]={ 3.61600e+00, 1.26800e+00, -5.94000e-01}
40: x[ 65]={ 3.49200e+00, 1.34200e+00, -4.42000e-01}
40: x[ 66]={ 3.53000e+00, 1.44000e+00, -3.78000e-01}
40: x[ 67]={ 3.40500e+00, 1.25400e+00, -3.97000e-01}
40: x[ 68]={ 3.37100e+00, 1.18400e+00, -4.60000e-01}
40: x[ 69]={ 3.35600e+00, 1.25400e+00, -2.59000e-01}
40: x[ 70]={ 3.29800e+00, 1.33400e+00, -2.52000e-01}
40: x[ 71]={ 3.27600e+00, 1.12600e+00, -2.33000e-01}
40: x[ 72]={ 3.20000e+00, 1.12200e+00, -2.97000e-01}
40: x[ 73]={ 3.33600e+00, 1.04700e+00, -2.47000e-01}
40: x[ 74]={ 3.22100e+00, 1.12000e+00, -9.20000e-02}
40: x[ 75]={ 3.29700e+00, 1.11700e+00, -2.70000e-02}
40: x[ 76]={ 3.16500e+00, 1.20100e+00, -7.50000e-02}
40: x[ 77]={ 3.13800e+00, 1.00000e+00, -7.20000e-02}
40: x[ 78]={ 3.10400e+00, 9.99000e-01, 2.20000e-02}
40: x[ 79]={ 3.06000e+00, 1.00500e+00, -1.35000e-01}
40: x[ 80]={ 3.20600e+00, 8.75000e-01, -9.60000e-02}
40: x[ 81]={ 3.20200e+00, 8.40000e-01, -1.89000e-01}
40: x[ 82]={ 3.27300e+00, 8.01000e-01, -1.00000e-02}
40: x[ 83]={ 3.28400e+00, 8.33000e-01, 1.19000e-01}
40: x[ 84]={ 3.23900e+00, 9.16000e-01, 1.53000e-01}
40: x[ 85]={ 3.33600e+00, 7.75000e-01, 1.81000e-01}
40: x[ 86]={ 3.32500e+00, 6.84000e-01, -5.30000e-02}
40: x[ 87]={ 3.31100e+00, 6.55000e-01, -1.47000e-01}
40: x[ 88]={ 3.37600e+00, 6.26000e-01, 1.00000e-02}
40: x[ 89]={ 3.46700e+00, 1.27300e+00, -1.56000e-01}
40: x[ 90]={ 3.46700e+00, 1.36500e+00, -7.00000e-02}
40: x[ 91]={ 3.56700e+00, 1.18500e+00, -1.61000e-01}
40: x[ 92]={ 3.56700e+00, 1.11600e+00, -2.33000e-01}
40: x[ 93]={ 3.67800e+00, 1.18700e+00, -6.50000e-02}
40: x[ 94]={ 3.63100e+00, 1.20200e+00, 2.20000e-02}
40: x[ 95]={ 3.74900e+00, 1.05300e+00, -6.20000e-02}
40: x[ 96]={ 3.77000e+00, 1.03400e+00, -1.58000e-01}
40: x[ 97]={ 3.83400e+00, 1.07200e+00, -1.30000e-02}
40: x[ 98]={ 3.65400e+00, 9.20000e-01, 1.40000e-02}
40: x[ 99]={ 3.70750e+00, 8.35500e-01, 1.20000e-02}
40: x[ 100]={ 3.77500e+00, 1.30500e+00, -7.80000e-02}
40: x[ 101]={ 3.81500e+00, 1.36100e+00, 2.60000e-02}
40: x[ 102]={ 3.78600e+00, 1.34800e+00, -2.02000e-01}
40: x[ 103]={ 3.74000e+00, 1.30000e+00, -2.76000e-01}
40: x[ 104]={ 3.86800e+00, 1.46900e+00, -2.31000e-01}
40: x[ 105]={ 3.96000e+00, 1.45500e+00, -1.93000e-01}
40: x[ 106]={ 3.87800e+00, 1.48500e+00, -3.82000e-01}
40: x[ 107]={ 3.92300e+00, 1.40200e+00, -4.17000e-01}
40: x[ 108]={ 3.78500e+00, 1.48900e+00, -4.17000e-01}
40: x[ 109]={ 3.95400e+00, 1.60500e+00, -4.38000e-01}
40: x[ 110]={ 3.91300e+00, 1.68700e+00, -3.99000e-01}
40: x[ 111]={ 4.04900e+00, 1.59800e+00, -4.07000e-01}
40: x[ 112]={ 3.95800e+00, 1.62400e+00, -5.87000e-01}
40: x[ 113]={ 3.86700e+00, 1.56400e+00, -6.49000e-01}
40: x[ 114]={ 4.04200e+00, 1.69500e+00, -6.38000e-01}
40: x[ 115]={ 3.80500e+00, 1.59300e+00, -1.66000e-01}
40: x[ 116]={ 3.87400e+00, 1.67300e+00, -1.01000e-01}
40: x[ 117]={ 3.67400e+00, 1.60500e+00, -1.82000e-01}
40: x[ 118]={ 3.62600e+00, 1.53500e+00, -2.35000e-01}
40: x[ 119]={ 3.59600e+00, 1.71600e+00, -1.25000e-01}
40: x[ 120]={ 3.64000e+00, 1.80100e+00, -1.56000e-01}
40: x[ 121]={ 3.45300e+00, 1.71700e+00, -1.81000e-01}
40: x[ 122]={ 3.45700e+00, 1.72200e+00, -2.81000e-01}
40: x[ 123]={ 3.40600e+00, 1.63300e+00, -1.53000e-01}
40: x[ 124]={ 3.37200e+00, 1.83500e+00, -1.31000e-01}
40: x[ 125]={ 3.37800e+00, 1.84200e+00, -3.10000e-02}
40: x[ 126]={ 3.43000e+00, 1.96600e+00, -1.84000e-01}
40: x[ 127]={ 3.37600e+00, 2.04300e+00, -1.50000e-01}
40: x[ 128]={ 3.52400e+00, 1.97500e+00, -1.53000e-01}
40: x[ 129]={ 3.42700e+00, 1.96500e+00, -2.84000e-01}
40: x[ 130]={ 3.22500e+00, 1.81400e+00, -1.60000e-01}
40: x[ 131]={ 3.17200e+00, 1.89300e+00, -1.26000e-01}
40: x[ 132]={ 3.21100e+00, 1.80500e+00, -2.58000e-01}
40: x[ 133]={ 3.19300e+00, 1.73100e+00, -1.14000e-01}
40: x[ 134]={ 3.60500e+00, 1.71300e+00, 2.70000e-02}
40: x[ 135]={ 3.61600e+00, 1.81700e+00, 9.20000e-02}
40: x[ 136]={ 3.57500e+00, 1.59800e+00, 8.30000e-02}
40: x[ 137]={ 3.54600e+00, 1.52200e+00, 2.40000e-02}
40: x[ 138]={ 3.58400e+00, 1.57600e+00, 2.28000e-01}
40: x[ 139]={ 3.50800e+00, 1.62600e+00, 2.69000e-01}
40: x[ 140]={ 3.56600e+00, 1.42900e+00, 2.62000e-01}
40: x[ 141]={ 3.57200e+00, 1.41600e+00, 3.61000e-01}
40: x[ 142]={ 3.47600e+00, 1.39800e+00, 2.30000e-01}
40: x[ 143]={ 3.63700e+00, 1.37500e+00, 2.18000e-01}
40: x[ 144]={ 3.71400e+00, 1.63100e+00, 2.84000e-01}
40: x[ 145]={ 3.71500e+00, 1.69800e+00, 3.90000e-01}
40: x[ 146]={ 3.82700e+00, 1.59800e+00, 2.20000e-01}
40: x[ 147]={ 3.82000e+00, 1.53900e+00, 1.40000e-01}
40: x[ 148]={ 3.96100e+00, 1.64300e+00, 2.62000e-01}
40: x[ 149]={ 3.96900e+00, 1.61900e+00, 3.58000e-01}
40: x[ 150]={ 4.07100e+00, 1.57100e+00, 1.84000e-01}
40: x[ 151]={ 4.16000e+00, 1.60300e+00, 2.15000e-01}
40: x[ 152]={ 4.06400e+00, 1.47200e+00, 2.01000e-01}
40: x[ 153]={ 4.06000e+00, 1.58900e+00, 8.60000e-02}
40: x[ 154]={ 3.97400e+00, 1.79400e+00, 2.46000e-01}
40: x[ 155]={ 4.01900e+00, 1.85000e+00, 3.47000e-01}
40: v (156x3):
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40: v[ 3]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 4]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 5]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 6]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 7]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 8]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 9]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 10]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
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40: v[ 12]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 13]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 14]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 15]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 16]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
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40: v[ 29]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 30]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
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40: v[ 33]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 34]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 35]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 36]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 37]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 38]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 39]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 40]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 41]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 42]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 43]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 44]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 45]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 46]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 47]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 48]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 49]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 50]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 51]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 52]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 53]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 54]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 55]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 56]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 57]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 58]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 59]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 60]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 61]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 62]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 63]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 64]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 65]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 66]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 67]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 68]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 69]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 70]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 71]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 72]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 73]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 74]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 75]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 76]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 77]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 78]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 79]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 80]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 81]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 82]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 83]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 84]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 85]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 86]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 87]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 88]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 89]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 90]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 91]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 92]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 93]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 94]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 95]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 96]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 97]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 98]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 99]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 100]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 101]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 102]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 103]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 104]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 105]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 106]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 107]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 108]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 109]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 110]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 111]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 112]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 113]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 114]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 115]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 116]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 117]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 118]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 119]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 120]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 121]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 122]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 123]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 124]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 125]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 126]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 127]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 128]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 129]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 130]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 131]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 132]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 133]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 134]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 135]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 136]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 137]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 138]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 139]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 140]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 141]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 142]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 143]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 144]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 145]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 146]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 147]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 148]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 149]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 150]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 151]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 152]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 153]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 154]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 155]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: Group statistics
40: T-Coupling : 156 (total 156 atoms)
40: Energy Mon. : 156 (total 156 atoms)
40: Acceleration: 156 (total 156 atoms)
40: Freeze : 156 (total 156 atoms)
40: User1 : 156 (total 156 atoms)
40: User2 : 156 (total 156 atoms)
40: VCM : 156 (total 156 atoms)
40: Compressed X: 156 (total 156 atoms)
40: Or. Res. Fit: 156 (total 156 atoms)
40: QMMM : 156 (total 156 atoms)
40: [ OK ] DumpTest.WorksWithTpr (58 ms)
40: [ RUN ] DumpTest.WorksWithTprAndMdpWriting
40: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
40: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
40: [ OK ] DumpTest.WorksWithTprAndMdpWriting (7 ms)
40: [----------] 2 tests from DumpTest (65 ms total)
40:
40: [----------] 4 tests from ReportMethodsTest
40:
40: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]:
40: For a correct single-point energy evaluation with nsteps = 0, use
40: continuation = yes to avoid constraining the input coordinates.
40:
40: Setting the LD random seed to -576613915
40: Generated 330891 of the 330891 non-bonded parameter combinations
40: Generating 1-4 interactions: fudge = 0.5
40: Generated 330891 of the 330891 1-4 parameter combinations
40: Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
40:
40: NOTE 2 [file lysozyme.top, line 1465]:
40: System has non-zero total charge: 2.000000
40: Total charge should normally be an integer. See
40: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
40: for discussion on how close it should be to an integer.
40:
40:
40:
40: Number of degrees of freedom in T-Coupling group rest is 465.00
40:
40: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]:
40: NVE simulation with an initial temperature of zero: will use a Verlet
40: buffer of 10%. Check your energy drift!
40:
40:
40: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]:
40: You are using a plain Coulomb cut-off, which might produce artifacts.
40: You might want to consider using PME electrostatics.
40:
40:
40:
40: There were 4 notes
40: Analysing residue names:
40: There are: 10 Protein residues
40: Analysing Protein...
40: This run will generate roughly 0 Mb of data
40: [ RUN ] ReportMethodsTest.WritesCorrectHeadersFormated
40: [ OK ] ReportMethodsTest.WritesCorrectHeadersFormated (0 ms)
40: [ RUN ] ReportMethodsTest.WritesCorrectHeadersUnformatted
40: [ OK ] ReportMethodsTest.WritesCorrectHeadersUnformatted (0 ms)
40: [ RUN ] ReportMethodsTest.WritesCorrectInformation
40: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
40: [ OK ] ReportMethodsTest.WritesCorrectInformation (5 ms)
40: [ RUN ] ReportMethodsTest.ToolEndToEndTest
40: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
40: section: Methods
40: subsection: Simulation system
40: A system of 1 molecules (156 atoms) was simulated.
40:
40: subsection: Simulation settings
40: A total of 0 ns were simulated with a time step of 1 fs.
40: Neighbor searching was performed every 10 steps.
40: The Cut-off algorithm was used for electrostatic interactions.
40: with a cut-off of 1 nm.
40: A single cut-off of 1.1 nm was used for Van der Waals interactions.
40: [ OK ] ReportMethodsTest.ToolEndToEndTest (5 ms)
40: [----------] 4 tests from ReportMethodsTest (10 ms total)
40:
40: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset
40: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/0
40: Will write tng: Trajectory file (tng format)
40: Group 0 ( System) has 6 elements
40: Group 1 (FirstWaterMolecule) has 3 elements
40: Group 2 (SecondWaterMolecule) has 3 elements
40: Select a group: trr version: GMX_trn_file (single precision)
40:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
40:
40: Note that major changes are planned in future for trjconv, to improve usability and utility.
40: Select group for output
40: Selected 2: 'SecondWaterMolecule'
40: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/0 (15 ms)
40: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/1
40: Will write tng: Trajectory file (tng format)
40: Group 0 ( System) has 6 elements
40: Group 1 (FirstWaterMolecule) has 3 elements
40: Group 2 (SecondWaterMolecule) has 3 elements
40: Select a group:
Reading frame 0 time 0.000
40: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm)
40: -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
40:
40: Note that major changes are planned in future for trjconv, to improve usability and utility.
40: Select group for output
40: Selected 2: 'SecondWaterMolecule'
40: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/1 (15 ms)
40: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/2
40: Will write tng: Trajectory file (tng format)
40: Group 0 ( System) has 6 elements
40: Group 1 (FirstWaterMolecule) has 3 elements
40: Group 2 (SecondWaterMolecule) has 3 elements
40: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
40:
40: Note that major changes are planned in future for trjconv, to improve usability and utility.
40: Select group for output
40: Selected 2: 'SecondWaterMolecule'
40: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/2 (13 ms)
40: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/3
40: Will write tng: Trajectory file (tng format)
40: Group 0 ( System) has 6 elements
40: Group 1 (FirstWaterMolecule) has 3 elements
40: Group 2 (SecondWaterMolecule) has 3 elements
40: Select a group: Reading frames from gro file '', 6 atoms.
40:
Reading frame 0 time 0.000
40: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm)
40: -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
40:
40: Note that major changes are planned in future for trjconv, to improve usability and utility.
40: Select group for output
40: Selected 2: 'SecondWaterMolecule'
40: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/3 (14 ms)
40: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/4
40: Will write tng: Trajectory file (tng format)
40: Group 0 ( System) has 6 elements
40: Group 1 (FirstWaterMolecule) has 3 elements
40: Group 2 (SecondWaterMolecule) has 3 elements
40: Select a group: Reading frames from pdb file
Reading frame 0 time 0.000
40: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm)
40: -> frame 0 time 0.000
't= 0.00000', 6 atoms
40:
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
40:
40: Note that major changes are planned in future for trjconv, to improve usability and utility.
40: Select group for output
40: Selected 2: 'SecondWaterMolecule'
40: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/4 (14 ms)
40: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/5
40: Will write tng: Trajectory file (tng format)
40: Group 0 ( System) has 6 elements
40: Group 1 (FirstWaterMolecule) has 3 elements
40: Group 2 (SecondWaterMolecule) has 3 elements
40: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
40:
40: Note that major changes are planned in future for trjconv, to improve usability and utility.
40: Select group for output
40: Selected 2: 'SecondWaterMolecule'
40: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/5 (14 ms)
40: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset (85 ms total)
40:
40: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile
40: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/0
40: Will write trr: Trajectory in portable xdr format
40: Group 0 ( System) has 6 elements
40: Group 1 (FirstWaterMolecule) has 3 elements
40: Group 2 (SecondWaterMolecule) has 3 elements
40: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
40:
40: Note that major changes are planned in future for trjconv, to improve usability and utility.
40: Select group for output
40: Selected 2: 'SecondWaterMolecule'
40: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/0 (4 ms)
40: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/1
40: Will write trr: Trajectory in portable xdr format
40: Group 0 ( System) has 6 elements
40: Group 1 (FirstWaterMolecule) has 3 elements
40: Group 2 (SecondWaterMolecule) has 3 elements
40: Select a group:
Reading frame 0 time 0.000
40: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm)
40: -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
40:
40: Note that major changes are planned in future for trjconv, to improve usability and utility.
40: Select group for output
40: Selected 2: 'SecondWaterMolecule'
40: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/1 (4 ms)
40: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/2
40: Will write trr: Trajectory in portable xdr format
40: Group 0 ( System) has 6 elements
40: Group 1 (FirstWaterMolecule) has 3 elements
40: Group 2 (SecondWaterMolecule) has 3 elements
40: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
40:
40: Note that major changes are planned in future for trjconv, to improve usability and utility.
40: Select group for output
40: Selected 2: 'SecondWaterMolecule'
40: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/2 (4 ms)
40: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/3
40: Will write trr: Trajectory in portable xdr format
40: Group 0 ( System) has 6 elements
40: Group 1 (FirstWaterMolecule) has 3 elements
40: Group 2 (SecondWaterMolecule) has 3 elements
40: Select a group: Reading frames from gro file '', 6 atoms.
40:
Reading frame 0 time 0.000
40: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm)
40: -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
40:
40: Note that major changes are planned in future for trjconv, to improve usability and utility.
40: Select group for output
40: Selected 2: 'SecondWaterMolecule'
40: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/3 (4 ms)
40: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/4
40: Will write trr: Trajectory in portable xdr format
40: Group 0 ( System) has 6 elements
40: Group 1 (FirstWaterMolecule) has 3 elements
40: Group 2 (SecondWaterMolecule) has 3 elements
40: Select a group: Reading frames from pdb file
Reading frame 0 time 0.000
40: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm)
40: -> frame 0 time 0.000
't= 0.00000', 6 atoms
40:
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
40:
40: Note that major changes are planned in future for trjconv, to improve usability and utility.
40: Select group for output
40: Selected 2: 'SecondWaterMolecule'
40: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/4 (4 ms)
40: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/5
40: Will write trr: Trajectory in portable xdr format
40: Group 0 ( System) has 6 elements
40: Group 1 (FirstWaterMolecule) has 3 elements
40: Group 2 (SecondWaterMolecule) has 3 elements
40: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
40:
40: Note that major changes are planned in future for trjconv, to improve usability and utility.
40: Select group for output
40: Selected 2: 'SecondWaterMolecule'
40: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/5 (4 ms)
40: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile (24 ms total)
40:
40: [----------] Global test environment tear-down
40: [==========] 18 tests from 4 test cases ran. (7235 ms total)
40: [ PASSED ] 18 tests.
40/52 Test #40: ToolUnitTests ....................... Passed 7.31 sec
test 41
Start 41: FileIOTests
41: Test command: /<<PKGBUILDDIR>>/build/basic/bin/fileio-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/FileIOTests.xml"
41: Test timeout computed to be: 30
41: [==========] Running 33 tests from 8 test cases.
41: [----------] Global test environment set-up.
41: [----------] 2 tests from FileMD5Test
41: [ RUN ] FileMD5Test.CanComputeMD5
41: [ OK ] FileMD5Test.CanComputeMD5 (5 ms)
41: [ RUN ] FileMD5Test.ReturnsErrorIfFileModeIsWrong
41: [ OK ] FileMD5Test.ReturnsErrorIfFileModeIsWrong (1 ms)
41: [----------] 2 tests from FileMD5Test (6 ms total)
41:
41: [----------] 3 tests from MrcSerializer
41: [ RUN ] MrcSerializer.DefaultHeaderValuesAreSet
41: [ OK ] MrcSerializer.DefaultHeaderValuesAreSet (0 ms)
41: [ RUN ] MrcSerializer.DefaultHeaderHasRightSerialSize
41: [ OK ] MrcSerializer.DefaultHeaderHasRightSerialSize (1 ms)
41: [ RUN ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip
41: [ OK ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip (4 ms)
41: [----------] 3 tests from MrcSerializer (5 ms total)
41:
41: [----------] 4 tests from MrcDensityMap
41: [ RUN ] MrcDensityMap.RoundTripIsIdempotent
41: [ OK ] MrcDensityMap.RoundTripIsIdempotent (5 ms)
41: [ RUN ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent
41: [ OK ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent (1 ms)
41: [ RUN ] MrcDensityMap.ReadsCoordinateTransformationFromFile
41: [ OK ] MrcDensityMap.ReadsCoordinateTransformationFromFile (0 ms)
41: [ RUN ] MrcDensityMap.ReadsDensityDataFromFile
41: [ OK ] MrcDensityMap.ReadsDensityDataFromFile (30 ms)
41: [----------] 4 tests from MrcDensityMap (37 ms total)
41:
41: [----------] 8 tests from MrcDensityMapHeaderTest
41: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader
41: [ OK ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader (0 ms)
41: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsCorrect
41: [ OK ] MrcDensityMapHeaderTest.DataSizeIsCorrect (0 ms)
41: [ RUN ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid
41: [ OK ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid (1 ms)
41: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven
41: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven (0 ms)
41: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined
41: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined (0 ms)
41: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues
41: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues (0 ms)
41: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectExtents
41: [ OK ] MrcDensityMapHeaderTest.GetsCorrectExtents (0 ms)
41: [ RUN ] MrcDensityMapHeaderTest.IsSane
41: [ OK ] MrcDensityMapHeaderTest.IsSane (0 ms)
41: [----------] 8 tests from MrcDensityMapHeaderTest (1 ms total)
41:
41: [----------] 9 tests from ReadTest
41: [ RUN ] ReadTest.get_eint_ReadsInteger
41: [ OK ] ReadTest.get_eint_ReadsInteger (0 ms)
41: [ RUN ] ReadTest.get_eint_WarnsAboutFloat
41:
41: ERROR 1 [file unknown, line 0]:
41: Right hand side '0.8' for parameter 'test' in parameter file is not an
41: integer value
41:
41:
41: [ OK ] ReadTest.get_eint_WarnsAboutFloat (1 ms)
41: [ RUN ] ReadTest.get_eint_WarnsAboutString
41:
41: ERROR 1 [file unknown, line 0]:
41: Right hand side 'hello' for parameter 'test' in parameter file is not an
41: integer value
41:
41:
41: [ OK ] ReadTest.get_eint_WarnsAboutString (0 ms)
41: [ RUN ] ReadTest.get_eint64_ReadsInteger
41: [ OK ] ReadTest.get_eint64_ReadsInteger (0 ms)
41: [ RUN ] ReadTest.get_eint64_WarnsAboutFloat
41:
41: ERROR 1 [file unknown, line 0]:
41: Right hand side '0.8' for parameter 'test' in parameter file is not an
41: integer value
41:
41:
41: [ OK ] ReadTest.get_eint64_WarnsAboutFloat (0 ms)
41: [ RUN ] ReadTest.get_eint64_WarnsAboutString
41:
41: ERROR 1 [file unknown, line 0]:
41: Right hand side 'hello' for parameter 'test' in parameter file is not an
41: integer value
41:
41:
41: [ OK ] ReadTest.get_eint64_WarnsAboutString (0 ms)
41: [ RUN ] ReadTest.get_ereal_ReadsInteger
41: [ OK ] ReadTest.get_ereal_ReadsInteger (0 ms)
41: [ RUN ] ReadTest.get_ereal_ReadsFloat
41: [ OK ] ReadTest.get_ereal_ReadsFloat (0 ms)
41: [ RUN ] ReadTest.get_ereal_WarnsAboutString
41:
41: ERROR 1 [file unknown, line 0]:
41: Right hand side 'hello' for parameter 'test' in parameter file is not a
41: real value
41:
41:
41: [ OK ] ReadTest.get_ereal_WarnsAboutString (0 ms)
41: [----------] 9 tests from ReadTest (1 ms total)
41:
41: [----------] 1 test from FileIOXdrSerializerTest
41: [ RUN ] FileIOXdrSerializerTest.SizeIsCorrect
41: [ OK ] FileIOXdrSerializerTest.SizeIsCorrect (2 ms)
41: [----------] 1 test from FileIOXdrSerializerTest (2 ms total)
41:
41: [----------] 2 tests from TngTest
41: [ RUN ] TngTest.CanOpenTngFile
41: TNG library: Cannot open file spc2-traj.tng. /<<PKGBUILDDIR>>/src/external/tng_io/src/lib/tng_io.c: 890
41: TNG library: Cannot open file spc2-traj.tng. /<<PKGBUILDDIR>>/src/external/tng_io/src/lib/tng_io.c: 890
41: [ OK ] TngTest.CanOpenTngFile (0 ms)
41: [ RUN ] TngTest.CloseBeforeOpenIsNotFatal
41: [ OK ] TngTest.CloseBeforeOpenIsNotFatal (0 ms)
41: [----------] 2 tests from TngTest (0 ms total)
41:
41: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest
41: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0
41: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 (3 ms)
41: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1
41: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 (2 ms)
41: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2
41: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 (9 ms)
41: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3
41: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 (3 ms)
41: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest (18 ms total)
41:
41: [----------] Global test environment tear-down
41: [==========] 33 tests from 8 test cases ran. (70 ms total)
41: [ PASSED ] 33 tests.
41/52 Test #41: FileIOTests ......................... Passed 0.14 sec
test 42
Start 42: SelectionUnitTests
42: Test command: /<<PKGBUILDDIR>>/build/basic/bin/selection-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/SelectionUnitTests.xml"
42: Test timeout computed to be: 30
42: [==========] Running 192 tests from 11 test cases.
42: [----------] Global test environment set-up.
42: [----------] 1 test from IndexGroupTest
42: [ RUN ] IndexGroupTest.RemovesDuplicates
42: [ OK ] IndexGroupTest.RemovesDuplicates (0 ms)
42: [----------] 1 test from IndexGroupTest (0 ms total)
42:
42: [----------] 15 tests from IndexBlockTest
42: [ RUN ] IndexBlockTest.CreatesUnknownBlock
42: [ OK ] IndexBlockTest.CreatesUnknownBlock (19 ms)
42: [ RUN ] IndexBlockTest.CreatesAtomBlock
42: [ OK ] IndexBlockTest.CreatesAtomBlock (9 ms)
42: [ RUN ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology
42: [ OK ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology (1 ms)
42: [ RUN ] IndexBlockTest.CreatesResidueBlocksForComplexTopology
42: [ OK ] IndexBlockTest.CreatesResidueBlocksForComplexTopology (23 ms)
42: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology
42: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology (1 ms)
42: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology
42: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology (2 ms)
42: [ RUN ] IndexBlockTest.CreatesSingleBlock
42: [ OK ] IndexBlockTest.CreatesSingleBlock (1 ms)
42: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksPositive
42: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksPositive (1 ms)
42: [ RUN ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive
42: [ OK ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive (0 ms)
42: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksNegative
42: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksNegative (0 ms)
42: [ RUN ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial
42: [ OK ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial (0 ms)
42: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive
42: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive (0 ms)
42: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative
42: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative (0 ms)
42: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive
42: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive (1 ms)
42: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative
42: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative (0 ms)
42: [----------] 15 tests from IndexBlockTest (58 ms total)
42:
42: [----------] 11 tests from IndexMapTest
42: [ RUN ] IndexMapTest.InitializesAtomBlock
42: [ OK ] IndexMapTest.InitializesAtomBlock (2 ms)
42: [ RUN ] IndexMapTest.InitializesOrgIdGroupAtom
42: [ OK ] IndexMapTest.InitializesOrgIdGroupAtom (1 ms)
42: [ RUN ] IndexMapTest.InitializesOrgIdGroupSingle
42: [ OK ] IndexMapTest.InitializesOrgIdGroupSingle (1 ms)
42: [ RUN ] IndexMapTest.InitializesOrgIdGroupResidue
42: [ OK ] IndexMapTest.InitializesOrgIdGroupResidue (2 ms)
42: [ RUN ] IndexMapTest.InitializesOrgIdGroupMolecule
42: [ OK ] IndexMapTest.InitializesOrgIdGroupMolecule (1 ms)
42: [ RUN ] IndexMapTest.InitializesOrgIdGroupAll
42: [ OK ] IndexMapTest.InitializesOrgIdGroupAll (1 ms)
42: [ RUN ] IndexMapTest.InitializesMoleculeBlock
42: [ OK ] IndexMapTest.InitializesMoleculeBlock (1 ms)
42: [ RUN ] IndexMapTest.MapsSingleBlock
42: [ OK ] IndexMapTest.MapsSingleBlock (1 ms)
42: [ RUN ] IndexMapTest.MapsResidueBlocks
42: [ OK ] IndexMapTest.MapsResidueBlocks (14 ms)
42: [ RUN ] IndexMapTest.MapsResidueBlocksWithMask
42: [ OK ] IndexMapTest.MapsResidueBlocksWithMask (2 ms)
42: [ RUN ] IndexMapTest.HandlesMultipleRequests
42: [ OK ] IndexMapTest.HandlesMultipleRequests (3 ms)
42: [----------] 11 tests from IndexMapTest (30 ms total)
42:
42: [----------] 3 tests from IndexGroupsAndNamesTest
42: [ RUN ] IndexGroupsAndNamesTest.containsNames
42: [ OK ] IndexGroupsAndNamesTest.containsNames (1 ms)
42: [ RUN ] IndexGroupsAndNamesTest.throwsWhenNameMissing
42: [ OK ] IndexGroupsAndNamesTest.throwsWhenNameMissing (0 ms)
42: [ RUN ] IndexGroupsAndNamesTest.groupIndicesCorrect
42: [ OK ] IndexGroupsAndNamesTest.groupIndicesCorrect (1 ms)
42: [----------] 3 tests from IndexGroupsAndNamesTest (2 ms total)
42:
42: [----------] 15 tests from NeighborhoodSearchTest
42: [ RUN ] NeighborhoodSearchTest.SimpleSearch
42: [ OK ] NeighborhoodSearchTest.SimpleSearch (68 ms)
42: [ RUN ] NeighborhoodSearchTest.SimpleSearchXY
42: [ OK ] NeighborhoodSearchTest.SimpleSearchXY (67 ms)
42: [ RUN ] NeighborhoodSearchTest.GridSearchBox
42: [ OK ] NeighborhoodSearchTest.GridSearchBox (12 ms)
42: [ RUN ] NeighborhoodSearchTest.GridSearchTriclinic
42: [ OK ] NeighborhoodSearchTest.GridSearchTriclinic (43 ms)
42: [ RUN ] NeighborhoodSearchTest.GridSearch2DPBC
42: [ OK ] NeighborhoodSearchTest.GridSearch2DPBC (21 ms)
42: [ RUN ] NeighborhoodSearchTest.GridSearchNoPBC
42: [ OK ] NeighborhoodSearchTest.GridSearchNoPBC (10 ms)
42: [ RUN ] NeighborhoodSearchTest.GridSearchXYBox
42: [ OK ] NeighborhoodSearchTest.GridSearchXYBox (12 ms)
42: [ RUN ] NeighborhoodSearchTest.SimpleSelfPairsSearch
42: [ OK ] NeighborhoodSearchTest.SimpleSelfPairsSearch (0 ms)
42: [ RUN ] NeighborhoodSearchTest.GridSelfPairsSearch
42: [ OK ] NeighborhoodSearchTest.GridSelfPairsSearch (185 ms)
42: [ RUN ] NeighborhoodSearchTest.HandlesConcurrentSearches
42: [ OK ] NeighborhoodSearchTest.HandlesConcurrentSearches (0 ms)
42: [ RUN ] NeighborhoodSearchTest.HandlesNoPBC
42: [ OK ] NeighborhoodSearchTest.HandlesNoPBC (0 ms)
42: [ RUN ] NeighborhoodSearchTest.HandlesNullPBC
42: [ OK ] NeighborhoodSearchTest.HandlesNullPBC (0 ms)
42: [ RUN ] NeighborhoodSearchTest.HandlesSkippingPairs
42: [ OK ] NeighborhoodSearchTest.HandlesSkippingPairs (0 ms)
42: [ RUN ] NeighborhoodSearchTest.SimpleSearchExclusions
42: [ OK ] NeighborhoodSearchTest.SimpleSearchExclusions (16 ms)
42: [ RUN ] NeighborhoodSearchTest.GridSearchExclusions
42: [ OK ] NeighborhoodSearchTest.GridSearchExclusions (4 ms)
42: [----------] 15 tests from NeighborhoodSearchTest (440 ms total)
42:
42: [----------] 12 tests from PositionCalculationTest
42: [ RUN ] PositionCalculationTest.ComputesAtomPositions
42: [ OK ] PositionCalculationTest.ComputesAtomPositions (3 ms)
42: [ RUN ] PositionCalculationTest.ComputesResidueCOGPositions
42: [ OK ] PositionCalculationTest.ComputesResidueCOGPositions (2 ms)
42: [ RUN ] PositionCalculationTest.ComputesResidueCOMPositions
42: [ OK ] PositionCalculationTest.ComputesResidueCOMPositions (2 ms)
42: [ RUN ] PositionCalculationTest.ComputesGroupCOGPositions
42: [ OK ] PositionCalculationTest.ComputesGroupCOGPositions (1 ms)
42: [ RUN ] PositionCalculationTest.ComputesGroupCOMPositions
42: [ OK ] PositionCalculationTest.ComputesGroupCOMPositions (1 ms)
42: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteWhole
42: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteWhole (2 ms)
42: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteMax
42: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteMax (1 ms)
42: [ RUN ] PositionCalculationTest.ComputesPositionMask
42: [ OK ] PositionCalculationTest.ComputesPositionMask (1 ms)
42: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms
42: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms (1 ms)
42: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms2
42: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms2 (1 ms)
42: [ RUN ] PositionCalculationTest.HandlesIdenticalStaticCalculations
42: [ OK ] PositionCalculationTest.HandlesIdenticalStaticCalculations (2 ms)
42: [ RUN ] PositionCalculationTest.HandlesOverlappingStaticCalculations
42: [ OK ] PositionCalculationTest.HandlesOverlappingStaticCalculations (1 ms)
42: [----------] 12 tests from PositionCalculationTest (24 ms total)
42:
42: [----------] 29 tests from SelectionCollectionTest
42: [ RUN ] SelectionCollectionTest.HandlesNoSelections
42: [ OK ] SelectionCollectionTest.HandlesNoSelections (1 ms)
42: [ RUN ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType
42: [ OK ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType (2 ms)
42: [ RUN ] SelectionCollectionTest.HandlesVelocityAndForceRequests
42: [ OK ] SelectionCollectionTest.HandlesVelocityAndForceRequests (2 ms)
42: [ RUN ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry
42: [ OK ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry (2 ms)
42: [ RUN ] SelectionCollectionTest.ParsesSelectionsFromFile
42: [ OK ] SelectionCollectionTest.ParsesSelectionsFromFile (1 ms)
42: [ RUN ] SelectionCollectionTest.HandlesAtypicalWhitespace
42: [ OK ] SelectionCollectionTest.HandlesAtypicalWhitespace (1 ms)
42: [ RUN ] SelectionCollectionTest.HandlesInvalidRegularExpressions
42: [ OK ] SelectionCollectionTest.HandlesInvalidRegularExpressions (3 ms)
42: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue
42: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue (1 ms)
42: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue2
42: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue2 (2 ms)
42: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue3
42: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue3 (1 ms)
42: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1
42: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 (2 ms)
42: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2
42: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 (2 ms)
42: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1
42: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 (1 ms)
42: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2
42: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 (2 ms)
42: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReference
42: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReference (3 ms)
42: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed
42: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed (1 ms)
42: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup
42: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup (2 ms)
42: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed
42: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed (1 ms)
42: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2
42: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 (2 ms)
42: [ RUN ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo
42: [ OK ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo (2 ms)
42: [ RUN ] SelectionCollectionTest.RecoversFromMissingAtomTypes
42: [ OK ] SelectionCollectionTest.RecoversFromMissingAtomTypes (2 ms)
42: [ RUN ] SelectionCollectionTest.RecoversFromMissingPDBInfo
42: [ OK ] SelectionCollectionTest.RecoversFromMissingPDBInfo (2 ms)
42: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation
42: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation (1 ms)
42: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation2
42: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation2 (2 ms)
42: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation3
42: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation3 (2 ms)
42: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets
42: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets (2 ms)
42: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2
42: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 (2 ms)
42: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3
42: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 (2 ms)
42: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4
42: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 (2 ms)
42: [----------] 29 tests from SelectionCollectionTest (52 ms total)
42:
42: [----------] 14 tests from SelectionCollectionInteractiveTest
42: [ RUN ] SelectionCollectionInteractiveTest.HandlesBasicInput
42: [ OK ] SelectionCollectionInteractiveTest.HandlesBasicInput (3 ms)
42: [ RUN ] SelectionCollectionInteractiveTest.HandlesContinuation
42: [ OK ] SelectionCollectionInteractiveTest.HandlesContinuation (2 ms)
42: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput
42: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput (2 ms)
42: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput
42: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput (2 ms)
42: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups
42: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups (4 ms)
42: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections
42: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections (3 ms)
42: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus
42: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus (3 ms)
42: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus
42: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus (3 ms)
42: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus
42: [ OK ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus (2 ms)
42: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline
42: [ OK ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline (2 ms)
42: [ RUN ] SelectionCollectionInteractiveTest.HandlesEmptySelections
42: [ OK ] SelectionCollectionInteractiveTest.HandlesEmptySelections (3 ms)
42: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine
42: [ OK ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine (2 ms)
42: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput
42: [ OK ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput (2 ms)
42: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively
42: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively (2 ms)
42: [----------] 14 tests from SelectionCollectionInteractiveTest (37 ms total)
42:
42: [----------] 66 tests from SelectionCollectionDataTest
42: [ RUN ] SelectionCollectionDataTest.HandlesAllNone
42: [ OK ] SelectionCollectionDataTest.HandlesAllNone (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesAtomnr
42: [ OK ] SelectionCollectionDataTest.HandlesAtomnr (2 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesResnr
42: [ OK ] SelectionCollectionDataTest.HandlesResnr (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesResIndex
42: [ OK ] SelectionCollectionDataTest.HandlesResIndex (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesMolIndex
42: [ OK ] SelectionCollectionDataTest.HandlesMolIndex (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesAtomname
42: [ OK ] SelectionCollectionDataTest.HandlesAtomname (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesPdbAtomname
42: [ OK ] SelectionCollectionDataTest.HandlesPdbAtomname (4 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesAtomtype
42: [ OK ] SelectionCollectionDataTest.HandlesAtomtype (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesChain
42: [ OK ] SelectionCollectionDataTest.HandlesChain (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesMass
42: [ OK ] SelectionCollectionDataTest.HandlesMass (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesCharge
42: [ OK ] SelectionCollectionDataTest.HandlesCharge (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesAltLoc
42: [ OK ] SelectionCollectionDataTest.HandlesAltLoc (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesInsertCode
42: [ OK ] SelectionCollectionDataTest.HandlesInsertCode (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesOccupancy
42: [ OK ] SelectionCollectionDataTest.HandlesOccupancy (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesBeta
42: [ OK ] SelectionCollectionDataTest.HandlesBeta (4 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesResname
42: [ OK ] SelectionCollectionDataTest.HandlesResname (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesCoordinateKeywords
42: [ OK ] SelectionCollectionDataTest.HandlesCoordinateKeywords (6 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesSameResidue
42: [ OK ] SelectionCollectionDataTest.HandlesSameResidue (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesSameResidueName
42: [ OK ] SelectionCollectionDataTest.HandlesSameResidueName (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesPositionKeywords
42: [ OK ] SelectionCollectionDataTest.HandlesPositionKeywords (8 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesDistanceKeyword
42: [ OK ] SelectionCollectionDataTest.HandlesDistanceKeyword (4 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesMinDistanceKeyword
42: [ OK ] SelectionCollectionDataTest.HandlesMinDistanceKeyword (4 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesWithinKeyword
42: [ OK ] SelectionCollectionDataTest.HandlesWithinKeyword (4 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword
42: [ OK ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword (26 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesPermuteModifier
42: [ OK ] SelectionCollectionDataTest.HandlesPermuteModifier (11 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesPlusModifier
42: [ OK ] SelectionCollectionDataTest.HandlesPlusModifier (11 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesMergeModifier
42: [ OK ] SelectionCollectionDataTest.HandlesMergeModifier (11 ms)
42: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndCharges
42: [ OK ] SelectionCollectionDataTest.ComputesMassesAndCharges (8 ms)
42: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology
42: [ OK ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology (5 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets
42: [ OK ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets (6 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesSelectionNames
42: [ OK ] SelectionCollectionDataTest.HandlesSelectionNames (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections
42: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections (6 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed
42: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed (5 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections
42: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections (8 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed
42: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed (5 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositions
42: [ OK ] SelectionCollectionDataTest.HandlesConstantPositions (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers
42: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesWithinConstantPositions
42: [ OK ] SelectionCollectionDataTest.HandlesWithinConstantPositions (4 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges
42: [ OK ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges (2 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingRealRanges
42: [ OK ] SelectionCollectionDataTest.HandlesOverlappingRealRanges (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode
42: [ OK ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesWildcardMatching
42: [ OK ] SelectionCollectionDataTest.HandlesWildcardMatching (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesRegexMatching
42: [ OK ] SelectionCollectionDataTest.HandlesRegexMatching (4 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesBasicBoolean
42: [ OK ] SelectionCollectionDataTest.HandlesBasicBoolean (5 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters
42: [ OK ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters (5 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions
42: [ OK ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame
42: [ OK ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame (4 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords
42: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords (4 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods
42: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods (4 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositions
42: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositions (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic
42: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesNumericComparisons
42: [ OK ] SelectionCollectionDataTest.HandlesNumericComparisons (7 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesArithmeticExpressions
42: [ OK ] SelectionCollectionDataTest.HandlesArithmeticExpressions (7 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesNumericVariables
42: [ OK ] SelectionCollectionDataTest.HandlesNumericVariables (5 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesComplexNumericVariables
42: [ OK ] SelectionCollectionDataTest.HandlesComplexNumericVariables (7 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariables
42: [ OK ] SelectionCollectionDataTest.HandlesPositionVariables (6 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariableInModifier
42: [ OK ] SelectionCollectionDataTest.HandlesPositionVariableInModifier (4 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionInVariable
42: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionInVariable (5 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables
42: [ OK ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables (5 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis
42: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis (6 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables
42: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables (4 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables
42: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables (4 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesUnusedVariables
42: [ OK ] SelectionCollectionDataTest.HandlesUnusedVariables (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups
42: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups
42: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2
42: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 (4 ms)
42: [----------] 66 tests from SelectionCollectionDataTest (337 ms total)
42:
42: [----------] 17 tests from SelectionOptionTest
42: [ RUN ] SelectionOptionTest.ParsesSimpleSelection
42: [ OK ] SelectionOptionTest.ParsesSimpleSelection (2 ms)
42: [ RUN ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired
42: [ OK ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired (1 ms)
42: [ RUN ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired
42: [ OK ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired (2 ms)
42: [ RUN ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired
42: [ OK ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired (2 ms)
42: [ RUN ] SelectionOptionTest.ChecksEmptySelections
42: [ OK ] SelectionOptionTest.ChecksEmptySelections (2 ms)
42: [ RUN ] SelectionOptionTest.ChecksEmptyDelayedSelections
42: [ OK ] SelectionOptionTest.ChecksEmptyDelayedSelections (1 ms)
42: [ RUN ] SelectionOptionTest.HandlesTooManySelections
42: [ OK ] SelectionOptionTest.HandlesTooManySelections (1 ms)
42: [ RUN ] SelectionOptionTest.HandlesTooFewSelections
42: [ OK ] SelectionOptionTest.HandlesTooFewSelections (2 ms)
42: [ RUN ] SelectionOptionTest.HandlesDefaultSelectionText
42: [ OK ] SelectionOptionTest.HandlesDefaultSelectionText (1 ms)
42: [ RUN ] SelectionOptionTest.HandlesAdjuster
42: [ OK ] SelectionOptionTest.HandlesAdjuster (1 ms)
42: [ RUN ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster
42: [ OK ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster (1 ms)
42: [ RUN ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster
42: [ OK ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster (2 ms)
42: [ RUN ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster
42: [ OK ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster (1 ms)
42: [ RUN ] SelectionOptionTest.HandlesDelayedRequiredSelection
42: [ OK ] SelectionOptionTest.HandlesDelayedRequiredSelection (1 ms)
42: [ RUN ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections
42: [ OK ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections (1 ms)
42: [ RUN ] SelectionOptionTest.HandlesDelayedOptionalSelection
42: [ OK ] SelectionOptionTest.HandlesDelayedOptionalSelection (2 ms)
42: [ RUN ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster
42: [ OK ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster (1 ms)
42: [----------] 17 tests from SelectionOptionTest (24 ms total)
42:
42: [----------] 9 tests from SelectionFileOptionTest
42: [ RUN ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile
42: [ OK ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile (1 ms)
42: [ RUN ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions
42: [ OK ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions (2 ms)
42: [ RUN ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile
42: [ OK ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile (1 ms)
42: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFile
42: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFile (1 ms)
42: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet
42: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet (2 ms)
42: [ RUN ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile
42: [ OK ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile (1 ms)
42: [ RUN ] SelectionFileOptionTest.GivesErrorWithNoFile
42: [ OK ] SelectionFileOptionTest.GivesErrorWithNoFile (1 ms)
42: [ RUN ] SelectionFileOptionTest.GivesErrorWithNonExistentFile
42: [ OK ] SelectionFileOptionTest.GivesErrorWithNonExistentFile (1 ms)
42: [ RUN ] SelectionFileOptionTest.GivesErrorWithMultipleFiles
42: [ OK ] SelectionFileOptionTest.GivesErrorWithMultipleFiles (2 ms)
42: [----------] 9 tests from SelectionFileOptionTest (13 ms total)
42:
42: [----------] Global test environment tear-down
42: [==========] 192 tests from 11 test cases ran. (1018 ms total)
42: [ PASSED ] 192 tests.
42/52 Test #42: SelectionUnitTests .................. Passed 1.11 sec
test 43
Start 43: MdrunTests
43: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrun-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunTests.xml"
43: Test timeout computed to be: 600
43: [==========] Running 84 tests from 21 test cases.
43: [----------] Global test environment set-up.
43: [----------] 4 tests from DensityFittingTest
43: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct
43: Setting the LD random seed to 1331389846
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group rest is 33.00
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43:
43: Steepest Descents:
43: Tolerance (Fmax) = 1.00000e+01
43: Number of steps = 2
43:
43: Energy minimization reached the maximum number of steps before the forces
43: reached the requested precision Fmax < 10.
43:
43: writing lowest energy coordinates.
43:
43: Steepest Descents did not converge to Fmax < 10 in 3 steps.
43: Potential Energy = -3.8565400e+03
43: Maximum force = 2.8846870e+03 on atom 3
43: Norm of force = 1.0754448e+03
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Last energy frame read 2 time 2.000 This run will generate roughly 0 Mb of data
43: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct (92 ms)
43: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy
43: Setting the LD random seed to -1177572198
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group rest is 33.00
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43:
43: Steepest Descents:
43: Tolerance (Fmax) = 1.00000e+01
43: Number of steps = 2
43:
43: Energy minimization reached the maximum number of steps before the forces
43: reached the requested precision Fmax < 10.
43:
43: writing lowest energy coordinates.
43:
43: Steepest Descents did not converge to Fmax < 10 in 3 steps.
43: Potential Energy = -2.7138666e+04
43: Maximum force = 4.3409717e+03 on atom 2
43: Norm of force = 1.2549793e+03
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Last energy frame read 2 time 2.000 This run will generate roughly 0 Mb of data
43: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy (37 ms)
43: [ RUN ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch
43:
43: [WARNING] /<<PKGBUILDDIR>>/src/external/googletest/googletest/src/gtest-death-test.cc:836:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads.
43: [ OK ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch (38 ms)
43: [ RUN ] DensityFittingTest.CheckpointWorks
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (2)
43:
43: Setting the LD random seed to -532774956
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group rest is 33.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]:
43: NVE simulation: will use the initial temperature of 68.810 K for
43: determining the Verlet buffer size
43:
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 2 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 68.8096 K
43: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.235 0.118 199.6
43: (ns/day) (hour/ns)
43: Performance: 2.205 10.884
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Overriding nsteps with value passed on the command line: 4 steps, 0.004 ps
43: Can not increase nstlist because an NVE ensemble is used
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 6 steps, 0.0 ps (continuing from step 2, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.245 0.123 199.6
43: (ns/day) (hour/ns)
43: Performance: 3.519 6.819
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.002
Last energy frame read 1 time 0.002 [ OK ] DensityFittingTest.CheckpointWorks (286 ms)
43: [----------] 4 tests from DensityFittingTest (454 ms total)
43:
43: [----------] 3 tests from GromppTest
43: [ RUN ] GromppTest.EmptyMdpFileWorks
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]:
43: For a correct single-point energy evaluation with nsteps = 0, use
43: continuation = yes to avoid constraining the input coordinates.
43:
43: Setting the LD random seed to 1865531797
43: Generated 8 of the 10 non-bonded parameter combinations
43: Excluding 2 bonded neighbours molecule type 'Methanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group rest is 12.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]:
43: NVE simulation: will use the initial temperature of 1046.791 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
43: Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: [ OK ] GromppTest.EmptyMdpFileWorks (23 ms)
43: [ RUN ] GromppTest.SimulatedAnnealingWorks
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]:
43: For a correct single-point energy evaluation with nsteps = 0, use
43: continuation = yes to avoid constraining the input coordinates.
43:
43: Setting the LD random seed to -1218734951
43: Generated 8 of the 10 non-bonded parameter combinations
43: Excluding 2 bonded neighbours molecule type 'Methanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Simulated annealing for group rest: Periodic, 4 timepoints
43: Time (ps) Temperature (K)
43: 0.0 298.0
43: 2.0 320.0
43: 4.0 320.0
43: 6.0 298.0
43: Number of degrees of freedom in T-Coupling group rest is 12.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]:
43: NVE simulation: will use the initial temperature of 1046.791 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
43: Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: [ OK ] GromppTest.SimulatedAnnealingWorks (23 ms)
43: [ RUN ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]:
43: For a correct single-point energy evaluation with nsteps = 0, use
43: continuation = yes to avoid constraining the input coordinates.
43:
43: Setting the LD random seed to -1736356798
43: Generated 8 of the 10 non-bonded parameter combinations
43: Excluding 2 bonded neighbours molecule type 'Methanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Simulated annealing for group Methanol: Single, 3 timepoints
43: Time (ps) Temperature (K)
43: 0.0 298.0
43: 3.0 280.0
43: 6.0- 270.0
43: Simulated annealing for group SOL: Periodic, 4 timepoints
43: Time (ps) Temperature (K)
43: 0.0 298.0
43: 2.0 320.0
43: 4.0 320.0
43: 6.0 298.0
43: Number of degrees of freedom in T-Coupling group Methanol is 7.20
43: Number of degrees of freedom in T-Coupling group SOL is 4.80
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]:
43: NVE simulation: will use the initial temperature of 1046.791 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
43: Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: [ OK ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups (23 ms)
43: [----------] 3 tests from GromppTest (69 ms total)
43:
43: [----------] 1 test from MdrunTest
43: [ RUN ] MdrunTest.WritesHelp
43: [ OK ] MdrunTest.WritesHelp (28 ms)
43: [----------] 1 test from MdrunTest (28 ms total)
43:
43: [----------] 1 test from OriresTest
43: [ RUN ] OriresTest.OriresCanRun
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun_input.mdp]:
43: The Berendsen thermostat does not generate the correct kinetic energy
43: distribution. You might want to consider using the V-rescale thermostat.
43:
43: Setting the LD random seed to 281136801
43: Generated 2145 of the 2145 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 2145 of the 2145 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 518.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Orientation restraints only supports a single rank. Choosing to use only a single thread-MPI rank.
43: Changing nstlist from 10 to 25, rlist from 1.054 to 1.164
43:
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'GUANINE NUCLEOTIDE-BINDING PROTEIN G(T), ALPHA-1'
43: 10 steps, 0.0 ps.
43: turning H bonds into constraints...
43: turning H bonds into constraints...
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
43: Calculated rlist for 1x1 atom pair-list as 1.073 nm, buffer size 0.073 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.054 nm, buffer size 0.054 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.350 0.175 199.6
43: (ns/day) (hour/ns)
43: Performance: 10.852 2.212
43: [ OK ] OriresTest.OriresCanRun (1739 ms)
43: [----------] 1 test from OriresTest (1739 ms total)
43:
43: [----------] 3 tests from PmeTest
43: [ RUN ] PmeTest.ReproducesEnergies
43: Setting the LD random seed to 495958104
43: Generated 8 of the 10 non-bonded parameter combinations
43: Excluding 2 bonded neighbours molecule type 'Methanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group rest is 12.00
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
43: NVE simulation: will use the initial temperature of 1046.791 K for
43: determining the Verlet buffer size
43:
43: Estimate for the relative computational load of the PME mesh part: 1.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
43: The optimal PME mesh load for parallel simulations is below 0.5
43: and for highly parallel simulations between 0.25 and 0.33,
43: for higher performance, increase the cut-off and the PME grid spacing.
43:
43:
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc-and-methanol'
43: 20 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
43: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: Calculating fourier grid dimensions for X Y Z
43: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.491 0.246 199.8
43: (ns/day) (hour/ns)
43: Performance: 7.388 3.249
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeAuto.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc-and-methanol'
43: 20 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.488 0.244 199.8
43: (ns/day) (hour/ns)
43: Performance: 7.431 3.230
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpu.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43:
43: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
43: starting mdrun 'spc-and-methanol'
43: 20 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.465 0.233 199.8
43: (ns/day) (hour/ns)
43: Performance: 7.803 3.076
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpuTune.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 [ OK ] PmeTest.ReproducesEnergies (10891 ms)
43: [ RUN ] PmeTest.ScalesTheBox
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
43: For a correct single-point energy evaluation with nsteps = 0, use
43: continuation = yes to avoid constraining the input coordinates.
43:
43: Setting the LD random seed to 320701003
43: Generated 8 of the 10 non-bonded parameter combinations
43: Excluding 2 bonded neighbours molecule type 'Methanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group rest is 12.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
43: NVE simulation: will use the initial temperature of 1046.791 K for
43: determining the Verlet buffer size
43:
43: Estimate for the relative computational load of the PME mesh part: 1.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
43: The optimal PME mesh load for parallel simulations is below 0.5
43: and for highly parallel simulations between 0.25 and 0.33,
43: for higher performance, increase the cut-off and the PME grid spacing.
43:
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc-and-methanol'
43: 0 steps, 0.0 ps.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.012 0.006 190.9
43: (ns/day) (hour/ns)
43: Performance: 13.462 1.783
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_spc-and-methanol_PmeOnCpu.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
43: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: Calculating fourier grid dimensions for X Y Z
43: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108
43: This run will generate roughly 0 Mb of data
43: [ OK ] PmeTest.ScalesTheBox (63 ms)
43: [ RUN ] PmeTest.ScalesTheBoxWithWalls
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
43: For a correct single-point energy evaluation with nsteps = 0, use
43: continuation = yes to avoid constraining the input coordinates.
43:
43: Setting the LD random seed to -743534998
43: Generated 8 of the 10 non-bonded parameter combinations
43: Excluding 2 bonded neighbours molecule type 'Methanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Searching the wall atom type(s)
43: Number of degrees of freedom in T-Coupling group rest is 13.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
43: NVE simulation: will use the initial temperature of 966.268 K for
43: determining the Verlet buffer size
43:
43: Estimate for the relative computational load of the PME mesh part: 1.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
43: The optimal PME mesh load for parallel simulations is below 0.5
43: and for highly parallel simulations between 0.25 and 0.33,
43: for higher performance, increase the cut-off and the PME grid spacing.
43:
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc-and-methanol'
43: 0 steps, 0.0 ps.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.054 0.027 197.2
43: (ns/day) (hour/ns)
43: Performance: 3.165 7.584
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_spc-and-methanol_PmeOnCpu.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K
43: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: Calculating fourier grid dimensions for X Y Z
43: Using a fourier grid of 28x28x128, spacing 0.108 0.108 0.118
43: This run will generate roughly 0 Mb of data
43: [ OK ] PmeTest.ScalesTheBoxWithWalls (31492 ms)
43: [----------] 3 tests from PmeTest (42446 ms total)
43:
43: [----------] 1 test from CompelTest
43: [ RUN ] CompelTest.SwapCanRun
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]:
43: The Berendsen thermostat does not generate the correct kinetic energy
43: distribution. You might want to consider using the V-rescale thermostat.
43:
43: Setting the LD random seed to 2002602177
43: Generated 330891 of the 330891 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 330891 of the 330891 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'Protein'
43: Excluding 3 bonded neighbours molecule type 'OCT'
43: Excluding 1 bonded neighbours molecule type 'NA'
43: Excluding 1 bonded neighbours molecule type 'CL'
43: Excluding 3 bonded neighbours molecule type 'Protein'
43: Excluding 3 bonded neighbours molecule type 'OCT'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Split0 group 'Ch0' contains 83 atoms.
43: Split1 group 'Ch1' contains 83 atoms.
43: Solvent group 'SOL' contains 11931 atoms.
43: Swap group 'NA+' contains 19 atoms.
43: Swap group 'CL-' contains 19 atoms.
43: Number of degrees of freedom in T-Coupling group System is 27869.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]:
43: Removing center of mass motion in the presence of position restraints
43: might cause artifacts. When you are using position restraints to
43: equilibrate a macro-molecule, the artifacts are usually negligible.
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: SWAP: Determining initial numbers of ions per compartment.
43: SWAP: Setting pointers for checkpoint writing
43: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules
43: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules
43: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules
43: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules
43: starting mdrun 'Channel_coco in octane membrane'
43: 2 steps, 0.0 ps.
43: turning all bonds into constraints...
43: turning all bonds into constraints...
43: turning all bonds into constraints...
43: turning all bonds into constraints...
43: turning all bonds into constraints...
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
43: Calculated rlist for 1x1 atom pair-list as 1.314 nm, buffer size 0.314 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.260 nm, buffer size 0.260 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 1 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 5.222 2.611 200.0
43: (ns/day) (hour/ns)
43: Performance: 0.496 48.359
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Overriding nsteps with value passed on the command line: 2 steps, 0.01 ps
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: SWAP: Setting pointers for checkpoint writing
43: SWAP: Copying channel fluxes from checkpoint file data
43: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules
43: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules
43: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules
43: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules
43: starting mdrun 'Channel_coco in octane membrane'
43: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 4.558 2.280 200.0
43: (ns/day) (hour/ns)
43: Performance: 0.569 42.214
43: [ OK ] CompelTest.SwapCanRun (9829 ms)
43: [----------] 1 test from CompelTest (9829 ms total)
43:
43: [----------] 6 tests from BondedInteractionsTest
43: [ RUN ] BondedInteractionsTest.NormalBondWorks
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]:
43: For a correct single-point energy evaluation with nsteps = 0, use
43: continuation = yes to avoid constraining the input coordinates.
43:
43: Setting the LD random seed to 146336460
43: Generated 3 of the 3 non-bonded parameter combinations
43: Excluding 3 bonded neighbours molecule type 'butane'
43:
43: NOTE 2 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]:
43: In moleculetype 'butane' 2 atoms are not bound by a potential or
43: constraint to any other atom in the same moleculetype. Although
43: technically this might not cause issues in a simulation, this often means
43: that the user forgot to add a bond/potential/constraint or put multiple
43: molecules in the same moleculetype definition by mistake. Run with -v to
43: get information for each atom.
43:
43: Number of degrees of freedom in T-Coupling group rest is 9.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]:
43: NVE simulation with an initial temperature of zero: will use a Verlet
43: buffer of 10%. Check your energy drift!
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
43:
43: Reading frames from gro file 'A single butane', 4 atoms.
43:
Reading frame 0 time 0.000
Last frame 0 time 0.000
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.003 0.002 185.9
43: (ns/day) (hour/ns)
43: Performance: 54.298 0.442
43: This run will generate roughly 0 Mb of data
43: [ OK ] BondedInteractionsTest.NormalBondWorks (59 ms)
43: [ RUN ] BondedInteractionsTest.TabulatedBondWorks
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]:
43: For a correct single-point energy evaluation with nsteps = 0, use
43: continuation = yes to avoid constraining the input coordinates.
43:
43: Setting the LD random seed to 2141322500
43: Generated 3 of the 3 non-bonded parameter combinations
43: Excluding 3 bonded neighbours molecule type 'butane'
43:
43: NOTE 2 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]:
43: In moleculetype 'butane' 2 atoms are not bound by a potential or
43: constraint to any other atom in the same moleculetype. Although
43: technically this might not cause issues in a simulation, this often means
43: that the user forgot to add a bond/potential/constraint or put multiple
43: molecules in the same moleculetype definition by mistake. Run with -v to
43: get information for each atom.
43:
43: Number of degrees of freedom in T-Coupling group rest is 9.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]:
43: NVE simulation with an initial temperature of zero: will use a Verlet
43: buffer of 10%. Check your energy drift!
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
43:
43: Reading frames from gro file 'A single butane', 4 atoms.
43:
Reading frame 0 time 0.000
Last frame 0 time 0.000
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.003 0.002 185.4
43: (ns/day) (hour/ns)
43: Performance: 53.387 0.450
43: This run will generate roughly 0 Mb of data
43: [ OK ] BondedInteractionsTest.TabulatedBondWorks (44 ms)
43: [ RUN ] BondedInteractionsTest.NormalAngleWorks
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]:
43: For a correct single-point energy evaluation with nsteps = 0, use
43: continuation = yes to avoid constraining the input coordinates.
43:
43: Setting the LD random seed to 1850968792
43: Generated 3 of the 3 non-bonded parameter combinations
43: Excluding 3 bonded neighbours molecule type 'butane'
43:
43: NOTE 2 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]:
43: In moleculetype 'butane' 4 atoms are not bound by a potential or
43: constraint to any other atom in the same moleculetype. Although
43: technically this might not cause issues in a simulation, this often means
43: that the user forgot to add a bond/potential/constraint or put multiple
43: molecules in the same moleculetype definition by mistake. Run with -v to
43: get information for each atom.
43:
43: Number of degrees of freedom in T-Coupling group rest is 9.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]:
43: NVE simulation with an initial temperature of zero: will use a Verlet
43: buffer of 10%. Check your energy drift!
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
43:
43: Reading frames from gro file 'A single butane', 4 atoms.
43:
Reading frame 0 time 0.000
Last frame 0 time 0.000
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.003 0.002 184.8
43: (ns/day) (hour/ns)
43: Performance: 55.572 0.432
43: This run will generate roughly 0 Mb of data
43: [ OK ] BondedInteractionsTest.NormalAngleWorks (35 ms)
43: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]:
43: For a correct single-point energy evaluation with nsteps = 0, use
43: continuation = yes to avoid constraining the input coordinates.
43:
43: Setting the LD random seed to -1776994153
43: Generated 3 of the 3 non-bonded parameter combinations
43: Excluding 3 bonded neighbours molecule type 'butane'
43:
43: NOTE 2 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]:
43: In moleculetype 'butane' 4 atoms are not bound by a potential or
43: constraint to any other atom in the same moleculetype. Although
43: technically this might not cause issues in a simulation, this often means
43: that the user forgot to add a bond/potential/constraint or put multiple
43: molecules in the same moleculetype definition by mistake. Run with -v to
43: get information for each atom.
43:
43: Number of degrees of freedom in T-Coupling group rest is 9.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]:
43: NVE simulation with an initial temperature of zero: will use a Verlet
43: buffer of 10%. Check your energy drift!
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
43:
43: Reading frames from gro file 'A single butane', 4 atoms.
43:
Reading frame 0 time 0.000
Last frame 0 time 0.000
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.003 0.002 185.6
43: (ns/day) (hour/ns)
43: Performance: 53.128 0.452
43: This run will generate roughly 0 Mb of data
43: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (45 ms)
43: [ RUN ] BondedInteractionsTest.NormalDihedralWorks
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]:
43: For a correct single-point energy evaluation with nsteps = 0, use
43: continuation = yes to avoid constraining the input coordinates.
43:
43: Setting the LD random seed to -1931259623
43: Generated 3 of the 3 non-bonded parameter combinations
43: Excluding 3 bonded neighbours molecule type 'butane'
43:
43: NOTE 2 [file BondedInteractionsTest_NormalDihedralWorks_butane1.top, line 31]:
43: In moleculetype 'butane' 4 atoms are not bound by a potential or
43: constraint to any other atom in the same moleculetype. Although
43: technically this might not cause issues in a simulation, this often means
43: that the user forgot to add a bond/potential/constraint or put multiple
43: molecules in the same moleculetype definition by mistake. Run with -v to
43: get information for each atom.
43:
43: Number of degrees of freedom in T-Coupling group rest is 9.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]:
43: NVE simulation with an initial temperature of zero: will use a Verlet
43: buffer of 10%. Check your energy drift!
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
43:
43: Reading frames from gro file 'A single butane', 4 atoms.
43:
Reading frame 0 time 0.000
Last frame 0 time 0.000
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.003 0.002 185.0
43: (ns/day) (hour/ns)
43: Performance: 55.183 0.435
43: This run will generate roughly 0 Mb of data
43: [ OK ] BondedInteractionsTest.NormalDihedralWorks (35 ms)
43: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]:
43: For a correct single-point energy evaluation with nsteps = 0, use
43: continuation = yes to avoid constraining the input coordinates.
43:
43: Setting the LD random seed to 1611746010
43: Generated 3 of the 3 non-bonded parameter combinations
43: Excluding 3 bonded neighbours molecule type 'butane'
43:
43: NOTE 2 [file BondedInteractionsTest_TabulatedDihedralWorks_butane1.top, line 31]:
43: In moleculetype 'butane' 4 atoms are not bound by a potential or
43: constraint to any other atom in the same moleculetype. Although
43: technically this might not cause issues in a simulation, this often means
43: that the user forgot to add a bond/potential/constraint or put multiple
43: molecules in the same moleculetype definition by mistake. Run with -v to
43: get information for each atom.
43:
43: Number of degrees of freedom in T-Coupling group rest is 9.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]:
43: NVE simulation with an initial temperature of zero: will use a Verlet
43: buffer of 10%. Check your energy drift!
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
43:
43: Reading frames from gro file 'A single butane', 4 atoms.
43:
Reading frame 0 time 0.000
Last frame 0 time 0.000
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.003 0.002 185.1
43: (ns/day) (hour/ns)
43: Performance: 53.895 0.445
43: This run will generate roughly 0 Mb of data
43: [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (45 ms)
43: [----------] 6 tests from BondedInteractionsTest (263 ms total)
43:
43: [----------] 6 tests from MdrunTerminationTest
43: [ RUN ] MdrunTerminationTest.CheckpointRestartAppendsByDefault
43: Setting the LD random seed to -1775226526
43: Generated 3 of the 3 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 3 of the 3 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 9.00
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There was 1 note
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 2 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.206 0.103 199.5
43: (ns/day) (hour/ns)
43: Performance: 2.509 9.566
43: Reading toplogy and stuff from /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Setting nsteps to 4
43: Writing statusfile with starting step 0 and length 4 steps...
43: time 0.000 and length 0.004 ps
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.261 0.131 199.6
43: (ns/day) (hour/ns)
43: Performance: 1.979 12.125
43: [ OK ] MdrunTerminationTest.CheckpointRestartAppendsByDefault (284 ms)
43: [ RUN ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts
43: Setting the LD random seed to 1069268689
43: Generated 3 of the 3 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 3 of the 3 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 9.00
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There was 1 note
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 10 to 1, rlist from 1.024 to 1
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 100 steps, 0.1 ps.
43:
43: Step 1: Run time exceeded 0.000 hours, will terminate the run within 2 steps
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.217 0.109 199.6
43: (ns/day) (hour/ns)
43: Performance: 2.388 10.052
43: Reading toplogy and stuff from /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Setting nsteps to 102
43: Writing statusfile with starting step 0 and length 102 steps...
43: time 0.000 and length 0.102 ps
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 102 steps, 0.1 ps (continuing from step 2, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.240 0.120 199.6
43: (ns/day) (hour/ns)
43: Performance: 72.464 0.331
43: [ OK ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (277 ms)
43: [ RUN ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend
43: Setting the LD random seed to -790899457
43: Generated 3 of the 3 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 3 of the 3 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 9.00
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There was 1 note
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 2 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.261 0.131 199.6
43: (ns/day) (hour/ns)
43: Performance: 1.982 12.111
43: Reading toplogy and stuff from /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Setting nsteps to 4
43: Writing statusfile with starting step 0 and length 4 steps...
43: time 0.000 and length 0.004 ps
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.217 0.109 199.8
43: (ns/day) (hour/ns)
43: Performance: 2.383 10.071
43: Reading toplogy and stuff from /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Setting nsteps to 6
43: Writing statusfile with starting step 0 and length 6 steps...
43: time 0.000 and length 0.006 ps
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 6 steps, 0.0 ps (continuing from step 4, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.209 0.105 199.4
43: (ns/day) (hour/ns)
43: Performance: 2.471 9.713
43: Reading toplogy and stuff from /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Setting nsteps to 8
43: Writing statusfile with starting step 0 and length 8 steps...
43: time 0.000 and length 0.008 ps
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 8 steps, 0.0 ps (continuing from step 6, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.216 0.108 199.7
43: (ns/day) (hour/ns)
43: Performance: 2.397 10.011
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 8 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.001 0.001 166.5
43: (ns/day) (hour/ns)
43: Performance: 116.598 0.206
43: [ OK ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend (548 ms)
43: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile
43: Setting the LD random seed to -1661484156
43: Generated 3 of the 3 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 3 of the 3 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 9.00
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There was 1 note
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 2 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.230 0.115 199.6
43: (ns/day) (hour/ns)
43: Performance: 2.247 10.683
43: Reading toplogy and stuff from /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Setting nsteps to 4
43: Writing statusfile with starting step 0 and length 4 steps...
43: time 0.000 and length 0.004 ps
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 4 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.194 0.097 199.3
43: (ns/day) (hour/ns)
43: Performance: 4.431 5.416
43: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile (263 ms)
43: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile
43: Setting the LD random seed to 1416941947
43: Generated 3 of the 3 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 3 of the 3 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 9.00
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There was 1 note
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 2 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.216 0.108 199.6
43: (ns/day) (hour/ns)
43: Performance: 2.392 10.032
43: Reading toplogy and stuff from /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Setting nsteps to 4
43: Writing statusfile with starting step 0 and length 4 steps...
43: time 0.000 and length 0.004 ps
43: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile (148 ms)
43: [ RUN ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles
43: Setting the LD random seed to 1016149960
43: Generated 3 of the 3 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 3 of the 3 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 9.00
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There was 1 note
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 2 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.186 0.093 199.5
43: (ns/day) (hour/ns)
43: Performance: 2.775 8.650
43: Reading toplogy and stuff from /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Setting nsteps to 4
43: Writing statusfile with starting step 0 and length 4 steps...
43: time 0.000 and length 0.004 ps
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.280 0.140 199.8
43: (ns/day) (hour/ns)
43: Performance: 1.849 12.980
43: [ OK ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles (286 ms)
43: [----------] 6 tests from MdrunTerminationTest (1807 ms total)
43:
43: [----------] 4 tests from MimicTest
43: [ RUN ] MimicTest.OneQuantumMol
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
43: For a correct single-point energy evaluation with nsteps = 0, use
43: continuation = yes to avoid constraining the input coordinates.
43:
43: Setting the LD random seed to 215256755
43: Generated 10 of the 10 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 10 of the 10 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group rest is 21.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
43: NVE simulation with an initial temperature of zero: will use a Verlet
43: buffer of 10%. Check your energy drift!
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
43:
43: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
43:
Reading frame 0 time 0.000
Last frame 0 time 0.000
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.003 0.002 187.5
43: (ns/day) (hour/ns)
43: Performance: 48.351 0.496
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
43: [ OK ] MimicTest.OneQuantumMol (40 ms)
43: [ RUN ] MimicTest.AllQuantumMol
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
43: For a correct single-point energy evaluation with nsteps = 0, use
43: continuation = yes to avoid constraining the input coordinates.
43:
43: Setting the LD random seed to 1920737736
43: Generated 10 of the 10 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 10 of the 10 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group rest is 21.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
43: NVE simulation with an initial temperature of zero: will use a Verlet
43: buffer of 10%. Check your energy drift!
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
43:
43: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
43:
Reading frame 0 time 0.000
Last frame 0 time 0.000
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.003 0.002 187.5
43: (ns/day) (hour/ns)
43: Performance: 48.493 0.495
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
43: [ OK ] MimicTest.AllQuantumMol (40 ms)
43: [ RUN ] MimicTest.TwoQuantumMol
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
43: For a correct single-point energy evaluation with nsteps = 0, use
43: continuation = yes to avoid constraining the input coordinates.
43:
43: Setting the LD random seed to -991363164
43: Generated 10 of the 10 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 10 of the 10 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group rest is 21.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
43: NVE simulation with an initial temperature of zero: will use a Verlet
43: buffer of 10%. Check your energy drift!
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
43:
43: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
43:
Reading frame 0 time 0.000
Last frame 0 time 0.000
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.003 0.002 187.7
43: (ns/day) (hour/ns)
43: Performance: 48.899 0.491
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
43: [ OK ] MimicTest.TwoQuantumMol (43 ms)
43: [ RUN ] MimicTest.BondCuts
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
43: For a correct single-point energy evaluation with nsteps = 0, use
43: continuation = yes to avoid constraining the input coordinates.
43:
43: Setting the LD random seed to -1335917505
43: Generated 2211 of the 2211 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 2211 of the 2211 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
43: Number of degrees of freedom in T-Coupling group rest is 66.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
43: NVE simulation: will use the initial temperature of 300.368 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/ala.gro'
43:
43: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms.
43:
Reading frame 0 time 0.000
Last frame 0 time 0.000
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.005 0.003 191.5
43: (ns/day) (hour/ns)
43: Performance: 30.589 0.785
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K
43: Calculated rlist for 1x1 atom pair-list as 1.034 nm, buffer size 0.034 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.025 nm, buffer size 0.025 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: [ OK ] MimicTest.BondCuts (171 ms)
43: [----------] 4 tests from MimicTest (294 ms total)
43:
43: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput
43: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0
43: Setting the LD random seed to -901639964
43: Generated 3 of the 3 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 3 of the 3 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group rest is 9.00
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]:
43: NVE simulation: will use the initial temperature of 2573.591 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 1 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K
43: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.310 0.155 199.7
43: (ns/day) (hour/ns)
43: Performance: 1.115 21.532
43:
Reading frame 0 time 0.000
43: # Atoms 6
43:
Reading frame 1 time 0.001
Last frame 1 time 0.001
43:
43:
43: Item #frames Timestep (ps)
43: Step 2 0.001
43: Time 2 0.001
43: Lambda 0
43: Coords 2 0.001
43: Velocities 0
43: Forces 0
43: Box 2 0.001
43: Checking file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.xtc
43: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 (195 ms)
43: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1
43: Setting the LD random seed to 413330734
43: Generated 3 of the 3 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 3 of the 3 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group rest is 9.00
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]:
43: NVE simulation: will use the initial temperature of 2573.591 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 1 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K
43: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.296 0.148 199.7
43: (ns/day) (hour/ns)
43: Performance: 1.165 20.592
43:
Reading frame 0 time 0.000
43: # Atoms 6
43:
Reading frame 1 time 0.001
Last frame 1 time 0.001
43:
43:
43: Item #frames Timestep (ps)
43: Step 2 0.001
43: Time 2 0.001
43: Lambda 0
43: Coords 2 0.001
43: Velocities 0
43: Forces 0
43: Box 2 0.001
43: Checking file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.xtc
43: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 (189 ms)
43: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2
43: Setting the LD random seed to 689899360
43: Generated 3 of the 3 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 3 of the 3 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group rest is 9.00
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]:
43: NVE simulation: will use the initial temperature of 2573.591 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 1 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K
43: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.341 0.171 199.7
43: (ns/day) (hour/ns)
43: Performance: 1.012 23.713
43:
Reading frame 0 time 0.000
43: # Atoms 3
43:
Reading frame 1 time 0.001
Last frame 1 time 0.001
43:
43:
43: Item #frames Timestep (ps)
43: Step 2 0.001
43: Time 2 0.001
43: Lambda 0
43: Coords 2 0.001
43: Velocities 0
43: Forces 0
43: Box 2 0.001
43: Checking file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.xtc
43: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 (211 ms)
43: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput (596 ms total)
43:
43: [----------] 12 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact
43: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: NVE simulation: will use the initial temperature of 68.810 K for
43: determining the Verlet buffer size
43:
43:
43: There were 3 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: NVE simulation: will use the initial temperature of 68.810 K for
43: determining the Verlet buffer size
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.336 0.168 199.7
43: (ns/day) (hour/ns)
43: Performance: 8.720 2.752
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.353 0.177 199.6
43: (ns/day) (hour/ns)
43: Performance: 4.399 5.456
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.365 0.183 199.7
43: (ns/day) (hour/ns)
43: Performance: 4.249 5.648
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (617 ms)
43: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: NVE simulation: will use the initial temperature of 68.810 K for
43: determining the Verlet buffer size
43:
43:
43: There were 3 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: NVE simulation: will use the initial temperature of 68.810 K for
43: determining the Verlet buffer size
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.287 0.144 199.7
43: (ns/day) (hour/ns)
43: Performance: 10.216 2.349
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.270 0.135 199.8
43: (ns/day) (hour/ns)
43: Performance: 5.764 4.164
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.247 0.124 199.8
43: (ns/day) (hour/ns)
43: Performance: 6.290 3.816
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (483 ms)
43: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.708 nm, buffer size 0.008 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.708 nm, buffer size 0.008 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.708 nm, buffer size 0.008 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.708 nm, buffer size 0.008 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.340 0.170 199.7
43: (ns/day) (hour/ns)
43: Performance: 8.618 2.785
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.290 0.145 199.5
43: (ns/day) (hour/ns)
43: Performance: 5.347 4.488
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.290 0.145 199.7
43: (ns/day) (hour/ns)
43: Performance: 5.360 4.478
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (544 ms)
43: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.342 0.171 199.7
43: (ns/day) (hour/ns)
43: Performance: 8.579 2.797
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.246 0.124 199.4
43: (ns/day) (hour/ns)
43: Performance: 6.296 3.812
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.246 0.123 199.6
43: (ns/day) (hour/ns)
43: Performance: 6.312 3.802
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (500 ms)
43: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 3 of the 3 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 3 of the 3 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 9.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
43: NVE simulation: will use the initial temperature of 2573.591 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 4 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 3 of the 3 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 3 of the 3 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 9.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
43: NVE simulation: will use the initial temperature of 2573.591 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 4 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K
43: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K
43: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.251 0.126 199.4
43: (ns/day) (hour/ns)
43: Performance: 11.668 2.057
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.246 0.123 199.4
43: (ns/day) (hour/ns)
43: Performance: 6.308 3.804
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.224 0.112 199.5
43: (ns/day) (hour/ns)
43: Performance: 6.942 3.457
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (444 ms)
43: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 3 of the 3 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 3 of the 3 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 9.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
43: NVE simulation: will use the initial temperature of 2573.591 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 4 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 3 of the 3 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 3 of the 3 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 9.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
43: NVE simulation: will use the initial temperature of 2573.591 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 4 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K
43: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K
43: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.273 0.137 199.8
43: (ns/day) (hour/ns)
43: Performance: 10.736 2.235
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.335 0.168 199.8
43: (ns/day) (hour/ns)
43: Performance: 4.632 5.181
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.312 0.156 199.8
43: (ns/day) (hour/ns)
43: Performance: 4.986 4.814
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (544 ms)
43: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 3 of the 3 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 3 of the 3 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 9.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 3 of the 3 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 3 of the 3 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 9.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.731 to 0.816
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 0.731 nm, buffer size 0.031 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 0.731 nm, buffer size 0.031 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.291 0.146 199.6
43: (ns/day) (hour/ns)
43: Performance: 10.079 2.381
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.731 to 0.816
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.288 0.144 199.4
43: (ns/day) (hour/ns)
43: Performance: 5.386 4.456
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.731 to 0.816
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.286 0.143 199.6
43: (ns/day) (hour/ns)
43: Performance: 5.430 4.420
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (522 ms)
43: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 3 of the 3 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 3 of the 3 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 9.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 3 of the 3 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 3 of the 3 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 9.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 8 to 40, rlist from 0.754 to 1.017
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.292 0.146 199.7
43: (ns/day) (hour/ns)
43: Performance: 10.049 2.388
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 8 to 40, rlist from 0.754 to 1.017
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.289 0.145 199.5
43: (ns/day) (hour/ns)
43: Performance: 5.374 4.466
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 8 to 40, rlist from 0.754 to 1.017
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.242 0.121 199.6
43: (ns/day) (hour/ns)
43: Performance: 6.409 3.745
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (500 ms)
43: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 2145 of the 2145 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 2145 of the 2145 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
43:
43: NOTE 3 [file unknown]:
43: You are using constraints on all bonds, whereas the forcefield has been
43: parametrized only with constraints involving hydrogen atoms. We suggest
43: using constraints = h-bonds instead, this will also improve performance.
43:
43: Cleaning up constraints and constant bonded interactions with virtual sites
43: Removed 18 Angles with virtual sites, 21 left
43: Removed 10 Proper Dih.s with virtual sites, 44 left
43: Converted 15 Constraints with virtual sites to connections, 7 left
43: Number of degrees of freedom in T-Coupling group System is 23.00
43:
43: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
43: NVE simulation: will use the initial temperature of 456.887 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
43: There are 9 non-linear virtual site constructions. Their contribution to
43: the energy error is approximated. In most cases this does not affect the
43: error significantly.
43:
43:
43: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 6 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 2145 of the 2145 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 2145 of the 2145 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
43:
43: NOTE 3 [file unknown]:
43: You are using constraints on all bonds, whereas the forcefield has been
43: parametrized only with constraints involving hydrogen atoms. We suggest
43: using constraints = h-bonds instead, this will also improve performance.
43:
43: Cleaning up constraints and constant bonded interactions with virtual sites
43: Removed 18 Angles with virtual sites, 21 left
43: Removed 10 Proper Dih.s with virtual sites, 44 left
43: Converted 15 Constraints with virtual sites to connections, 7 left
43: Number of degrees of freedom in T-Coupling group System is 23.00
43:
43: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
43: NVE simulation: will use the initial temperature of 456.887 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
43: There are 9 non-linear virtual site constructions. Their contribution to
43: the energy error is approximated. In most cases this does not affect the
43: error significantly.
43:
43:
43: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 6 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Alanine dipeptide in vacuo'
43: 16 steps, 0.0 ps.
43: turning all bonds into constraints...
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
43: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: turning all bonds into constraints...
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
43: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.287 0.144 199.5
43: (ns/day) (hour/ns)
43: Performance: 10.201 2.353
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Alanine dipeptide in vacuo'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.351 0.176 199.5
43: (ns/day) (hour/ns)
43: Performance: 4.423 5.426
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Alanine dipeptide in vacuo'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.393 0.197 199.6
43: (ns/day) (hour/ns)
43: Performance: 3.952 6.073
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_secondpart.part0002.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8 (790 ms)
43: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 2145 of the 2145 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 2145 of the 2145 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
43:
43: NOTE 3 [file unknown]:
43: You are using constraints on all bonds, whereas the forcefield has been
43: parametrized only with constraints involving hydrogen atoms. We suggest
43: using constraints = h-bonds instead, this will also improve performance.
43:
43: Cleaning up constraints and constant bonded interactions with virtual sites
43: Removed 18 Angles with virtual sites, 21 left
43: Removed 10 Proper Dih.s with virtual sites, 44 left
43: Converted 15 Constraints with virtual sites to connections, 7 left
43: Number of degrees of freedom in T-Coupling group System is 23.00
43:
43: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
43: NVE simulation: will use the initial temperature of 456.887 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
43: There are 9 non-linear virtual site constructions. Their contribution to
43: the energy error is approximated. In most cases this does not affect the
43: error significantly.
43:
43:
43: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 6 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 2145 of the 2145 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 2145 of the 2145 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
43:
43: NOTE 3 [file unknown]:
43: You are using constraints on all bonds, whereas the forcefield has been
43: parametrized only with constraints involving hydrogen atoms. We suggest
43: using constraints = h-bonds instead, this will also improve performance.
43:
43: Cleaning up constraints and constant bonded interactions with virtual sites
43: Removed 18 Angles with virtual sites, 21 left
43: Removed 10 Proper Dih.s with virtual sites, 44 left
43: Converted 15 Constraints with virtual sites to connections, 7 left
43: Number of degrees of freedom in T-Coupling group System is 23.00
43:
43: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
43: NVE simulation: will use the initial temperature of 456.887 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
43: There are 9 non-linear virtual site constructions. Their contribution to
43: the energy error is approximated. In most cases this does not affect the
43: error significantly.
43:
43:
43: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 6 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Alanine dipeptide in vacuo'
43: 16 steps, 0.0 ps.
43: turning all bonds into constraints...
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
43: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: turning all bonds into constraints...
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
43: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.368 0.184 199.6
43: (ns/day) (hour/ns)
43: Performance: 7.971 3.011
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Alanine dipeptide in vacuo'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.305 0.153 199.4
43: (ns/day) (hour/ns)
43: Performance: 5.082 4.723
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Alanine dipeptide in vacuo'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.306 0.153 199.5
43: (ns/day) (hour/ns)
43: Performance: 5.068 4.736
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_secondpart.part0002.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9 (745 ms)
43: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 2145 of the 2145 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 2145 of the 2145 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
43:
43: NOTE 3 [file unknown]:
43: You are using constraints on all bonds, whereas the forcefield has been
43: parametrized only with constraints involving hydrogen atoms. We suggest
43: using constraints = h-bonds instead, this will also improve performance.
43:
43: Cleaning up constraints and constant bonded interactions with virtual sites
43: Removed 18 Angles with virtual sites, 21 left
43: Removed 10 Proper Dih.s with virtual sites, 44 left
43: Converted 15 Constraints with virtual sites to connections, 7 left
43: Number of degrees of freedom in T-Coupling group System is 23.00
43:
43: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
43: There are 9 non-linear virtual site constructions. Their contribution to
43: the energy error is approximated. In most cases this does not affect the
43: error significantly.
43:
43:
43: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 5 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 2145 of the 2145 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 2145 of the 2145 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
43:
43: NOTE 3 [file unknown]:
43: You are using constraints on all bonds, whereas the forcefield has been
43: parametrized only with constraints involving hydrogen atoms. We suggest
43: using constraints = h-bonds instead, this will also improve performance.
43:
43: Cleaning up constraints and constant bonded interactions with virtual sites
43: Removed 18 Angles with virtual sites, 21 left
43: Removed 10 Proper Dih.s with virtual sites, 44 left
43: Converted 15 Constraints with virtual sites to connections, 7 left
43: Number of degrees of freedom in T-Coupling group System is 23.00
43:
43: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
43: There are 9 non-linear virtual site constructions. Their contribution to
43: the energy error is approximated. In most cases this does not affect the
43: error significantly.
43:
43:
43: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 5 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Alanine dipeptide in vacuo'
43: 16 steps, 0.0 ps.
43: turning all bonds into constraints...
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 0.748 nm, buffer size 0.048 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.744 nm, buffer size 0.044 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: turning all bonds into constraints...
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 0.748 nm, buffer size 0.048 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.744 nm, buffer size 0.044 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.293 0.147 199.5
43: (ns/day) (hour/ns)
43: Performance: 9.997 2.401
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Alanine dipeptide in vacuo'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.312 0.156 199.4
43: (ns/day) (hour/ns)
43: Performance: 4.974 4.825
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Alanine dipeptide in vacuo'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.546 0.273 199.8
43: (ns/day) (hour/ns)
43: Performance: 2.844 8.439
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_secondpart.part0002.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10 (1000 ms)
43: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 2145 of the 2145 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 2145 of the 2145 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
43:
43: NOTE 3 [file unknown]:
43: You are using constraints on all bonds, whereas the forcefield has been
43: parametrized only with constraints involving hydrogen atoms. We suggest
43: using constraints = h-bonds instead, this will also improve performance.
43:
43: Cleaning up constraints and constant bonded interactions with virtual sites
43: Removed 18 Angles with virtual sites, 21 left
43: Removed 10 Proper Dih.s with virtual sites, 44 left
43: Converted 15 Constraints with virtual sites to connections, 7 left
43: Number of degrees of freedom in T-Coupling group System is 23.00
43:
43: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
43: There are 9 non-linear virtual site constructions. Their contribution to
43: the energy error is approximated. In most cases this does not affect the
43: error significantly.
43:
43:
43: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 5 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 2145 of the 2145 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 2145 of the 2145 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
43:
43: NOTE 3 [file unknown]:
43: You are using constraints on all bonds, whereas the forcefield has been
43: parametrized only with constraints involving hydrogen atoms. We suggest
43: using constraints = h-bonds instead, this will also improve performance.
43:
43: Cleaning up constraints and constant bonded interactions with virtual sites
43: Removed 18 Angles with virtual sites, 21 left
43: Removed 10 Proper Dih.s with virtual sites, 44 left
43: Converted 15 Constraints with virtual sites to connections, 7 left
43: Number of degrees of freedom in T-Coupling group System is 23.00
43:
43: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
43: There are 9 non-linear virtual site constructions. Their contribution to
43: the energy error is approximated. In most cases this does not affect the
43: error significantly.
43:
43:
43: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 5 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Alanine dipeptide in vacuo'
43: 16 steps, 0.0 ps.
43: turning all bonds into constraints...
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: turning all bonds into constraints...
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.895 0.448 199.8
43: (ns/day) (hour/ns)
43: Performance: 3.279 7.320
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Alanine dipeptide in vacuo'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.501 0.251 199.6
43: (ns/day) (hour/ns)
43: Performance: 3.097 7.749
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Alanine dipeptide in vacuo'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.338 0.169 199.6
43: (ns/day) (hour/ns)
43: Performance: 4.597 5.220
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_secondpart.part0002.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11 (1244 ms)
43: [----------] 12 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact (7934 ms total)
43:
43: [----------] 4 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact
43: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 2485 of the 2485 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 2485 of the 2485 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'nonanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 79.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: NVE simulation: will use the initial temperature of 293.480 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 4 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 2485 of the 2485 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 2485 of the 2485 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'nonanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 79.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: NVE simulation: will use the initial temperature of 293.480 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 4 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun '30 system in water'
43: 16 steps, 0.0 ps.
43: turning H bonds into constraints...
43: turning H bonds into constraints...
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
43: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: turning H bonds into constraints...
43: turning H bonds into constraints...
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
43: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.382 0.191 199.5
43: (ns/day) (hour/ns)
43: Performance: 7.671 3.129
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun '30 system in water'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.526 0.264 199.3
43: (ns/day) (hour/ns)
43: Performance: 2.947 8.144
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun '30 system in water'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.368 0.185 199.5
43: (ns/day) (hour/ns)
43: Performance: 4.212 5.698
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (934 ms)
43: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 2485 of the 2485 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 2485 of the 2485 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'nonanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 79.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: NVE simulation: will use the initial temperature of 293.480 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 4 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 2485 of the 2485 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 2485 of the 2485 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'nonanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 79.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: NVE simulation: will use the initial temperature of 293.480 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 4 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun '30 system in water'
43: 16 steps, 0.0 ps.
43: turning H bonds into constraints...
43: turning H bonds into constraints...
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
43: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: turning H bonds into constraints...
43: turning H bonds into constraints...
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
43: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.552 0.276 199.9
43: (ns/day) (hour/ns)
43: Performance: 5.321 4.511
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun '30 system in water'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.349 0.175 199.8
43: (ns/day) (hour/ns)
43: Performance: 4.446 5.398
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun '30 system in water'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.677 0.338 199.9
43: (ns/day) (hour/ns)
43: Performance: 2.297 10.447
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (1033 ms)
43: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 2485 of the 2485 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 2485 of the 2485 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'nonanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 79.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 2485 of the 2485 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 2485 of the 2485 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'nonanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 79.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun '30 system in water'
43: 16 steps, 0.0 ps.
43: turning H bonds into constraints...
43: turning H bonds into constraints...
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: turning H bonds into constraints...
43: turning H bonds into constraints...
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.561 0.281 199.7
43: (ns/day) (hour/ns)
43: Performance: 5.231 4.588
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun '30 system in water'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.564 0.283 199.4
43: (ns/day) (hour/ns)
43: Performance: 2.750 8.727
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun '30 system in water'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.428 0.215 199.6
43: (ns/day) (hour/ns)
43: Performance: 3.625 6.620
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (1234 ms)
43: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 2485 of the 2485 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 2485 of the 2485 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'nonanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 79.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 2485 of the 2485 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 2485 of the 2485 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'nonanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 79.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun '30 system in water'
43: 16 steps, 0.0 ps.
43: turning H bonds into constraints...
43: turning H bonds into constraints...
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: turning H bonds into constraints...
43: turning H bonds into constraints...
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.423 0.212 199.6
43: (ns/day) (hour/ns)
43: Performance: 6.931 3.463
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun '30 system in water'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.575 0.288 199.4
43: (ns/day) (hour/ns)
43: Performance: 2.696 8.902
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun '30 system in water'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.597 0.299 199.7
43: (ns/day) (hour/ns)
43: Performance: 2.602 9.225
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (1167 ms)
43: [----------] 4 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact (4368 ms total)
43:
43: [----------] 6 tests from NVT/MdrunNoAppendContinuationIsExact
43: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: The Berendsen thermostat does not generate the correct kinetic energy
43: distribution. You might want to consider using the V-rescale thermostat.
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 3 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: The Berendsen thermostat does not generate the correct kinetic energy
43: distribution. You might want to consider using the V-rescale thermostat.
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.383 0.192 199.7
43: (ns/day) (hour/ns)
43: Performance: 7.668 3.130
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.469 0.235 199.6
43: (ns/day) (hour/ns)
43: Performance: 3.313 7.245
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.289 0.145 199.7
43: (ns/day) (hour/ns)
43: Performance: 5.366 4.472
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (654 ms)
43: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.543 0.272 199.8
43: (ns/day) (hour/ns)
43: Performance: 5.402 4.442
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.246 0.123 199.4
43: (ns/day) (hour/ns)
43: Performance: 6.307 3.805
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.225 0.113 199.6
43: (ns/day) (hour/ns)
43: Performance: 6.894 3.481
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (594 ms)
43: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 3 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.411 0.206 199.8
43: (ns/day) (hour/ns)
43: Performance: 7.141 3.361
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.268 0.135 199.3
43: (ns/day) (hour/ns)
43: Performance: 5.773 4.157
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.445 0.223 199.8
43: (ns/day) (hour/ns)
43: Performance: 3.487 6.882
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (660 ms)
43: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: The Berendsen thermostat does not generate the correct kinetic energy
43: distribution. You might want to consider using the V-rescale thermostat.
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 3 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: The Berendsen thermostat does not generate the correct kinetic energy
43: distribution. You might want to consider using the V-rescale thermostat.
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.298 0.149 199.7
43: (ns/day) (hour/ns)
43: Performance: 9.848 2.437
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.268 0.135 199.4
43: (ns/day) (hour/ns)
43: Performance: 5.781 4.152
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.468 0.234 199.8
43: (ns/day) (hour/ns)
43: Performance: 3.323 7.223
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (600 ms)
43: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.299 0.150 199.8
43: (ns/day) (hour/ns)
43: Performance: 9.800 2.449
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.425 0.213 199.9
43: (ns/day) (hour/ns)
43: Performance: 3.656 6.564
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.268 0.134 199.8
43: (ns/day) (hour/ns)
43: Performance: 5.790 4.145
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (578 ms)
43: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.476 0.238 199.8
43: (ns/day) (hour/ns)
43: Performance: 6.169 3.890
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.269 0.135 199.4
43: (ns/day) (hour/ns)
43: Performance: 5.773 4.157
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.290 0.145 199.7
43: (ns/day) (hour/ns)
43: Performance: 5.357 4.480
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (600 ms)
43: [----------] 6 tests from NVT/MdrunNoAppendContinuationIsExact (3687 ms total)
43:
43: [----------] 4 tests from NPH/MdrunNoAppendContinuationIsExact
43: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: NVE simulation: will use the initial temperature of 68.810 K for
43: determining the Verlet buffer size
43:
43:
43: There were 3 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: NVE simulation: will use the initial temperature of 68.810 K for
43: determining the Verlet buffer size
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.476 0.238 199.8
43: (ns/day) (hour/ns)
43: Performance: 6.161 3.895
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.291 0.146 199.3
43: (ns/day) (hour/ns)
43: Performance: 5.326 4.506
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.446 0.223 199.8
43: (ns/day) (hour/ns)
43: Performance: 3.485 6.887
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (689 ms)
43: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: NVE simulation: will use the initial temperature of 68.810 K for
43: determining the Verlet buffer size
43:
43:
43: There were 3 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: NVE simulation: will use the initial temperature of 68.810 K for
43: determining the Verlet buffer size
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.320 0.160 199.7
43: (ns/day) (hour/ns)
43: Performance: 9.152 2.622
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.358 0.179 199.5
43: (ns/day) (hour/ns)
43: Performance: 4.336 5.535
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.268 0.134 199.6
43: (ns/day) (hour/ns)
43: Performance: 5.791 4.144
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (556 ms)
43: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/2
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: NVE simulation: will use the initial temperature of 68.810 K for
43: determining the Verlet buffer size
43:
43:
43: There were 3 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: NVE simulation: will use the initial temperature of 68.810 K for
43: determining the Verlet buffer size
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.386 0.193 199.7
43: (ns/day) (hour/ns)
43: Performance: 7.592 3.161
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.291 0.146 199.3
43: (ns/day) (hour/ns)
43: Performance: 5.325 4.507
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.268 0.134 199.6
43: (ns/day) (hour/ns)
43: Performance: 5.792 4.143
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (555 ms)
43: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/3
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: NVE simulation: will use the initial temperature of 68.810 K for
43: determining the Verlet buffer size
43:
43:
43: There were 3 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: NVE simulation: will use the initial temperature of 68.810 K for
43: determining the Verlet buffer size
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.388 0.194 199.8
43: (ns/day) (hour/ns)
43: Performance: 7.561 3.174
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.270 0.135 199.8
43: (ns/day) (hour/ns)
43: Performance: 5.754 4.171
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.468 0.234 199.9
43: (ns/day) (hour/ns)
43: Performance: 3.319 7.231
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (645 ms)
43: [----------] 4 tests from NPH/MdrunNoAppendContinuationIsExact (2445 ms total)
43:
43: [----------] 12 tests from NPT/MdrunNoAppendContinuationIsExact
43: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: The Berendsen thermostat does not generate the correct kinetic energy
43: distribution. You might want to consider using the V-rescale thermostat.
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 3 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: The Berendsen thermostat does not generate the correct kinetic energy
43: distribution. You might want to consider using the V-rescale thermostat.
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.274 0.137 199.6
43: (ns/day) (hour/ns)
43: Performance: 10.715 2.240
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.468 0.235 199.6
43: (ns/day) (hour/ns)
43: Performance: 3.315 7.241
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.289 0.145 199.6
43: (ns/day) (hour/ns)
43: Performance: 5.370 4.469
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (600 ms)
43: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: The Berendsen thermostat does not generate the correct kinetic energy
43: distribution. You might want to consider using the V-rescale thermostat.
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 3 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: The Berendsen thermostat does not generate the correct kinetic energy
43: distribution. You might want to consider using the V-rescale thermostat.
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.297 0.149 199.6
43: (ns/day) (hour/ns)
43: Performance: 9.857 2.435
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.446 0.223 199.4
43: (ns/day) (hour/ns)
43: Performance: 3.480 6.897
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.267 0.134 199.6
43: (ns/day) (hour/ns)
43: Performance: 5.811 4.130
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (589 ms)
43: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.409 0.205 199.7
43: (ns/day) (hour/ns)
43: Performance: 7.179 3.343
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.246 0.123 199.2
43: (ns/day) (hour/ns)
43: Performance: 6.298 3.811
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.290 0.145 199.6
43: (ns/day) (hour/ns)
43: Performance: 5.362 4.476
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (555 ms)
43: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.520 0.260 199.8
43: (ns/day) (hour/ns)
43: Performance: 5.648 4.249
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.312 0.157 199.3
43: (ns/day) (hour/ns)
43: Performance: 4.965 4.834
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.467 0.234 199.8
43: (ns/day) (hour/ns)
43: Performance: 3.326 7.217
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (734 ms)
43: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
43: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
43:
43:
43: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
43: Using Berendsen pressure coupling invalidates the true ensemble for the
43: thermostat
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 3 notes
43:
43: There was 1 warning
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
43: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
43:
43:
43: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
43: Using Berendsen pressure coupling invalidates the true ensemble for the
43: thermostat
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 3 notes
43:
43: There was 1 warning
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.342 0.171 199.7
43: (ns/day) (hour/ns)
43: Performance: 8.567 2.801
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.468 0.235 199.6
43: (ns/day) (hour/ns)
43: Performance: 3.314 7.241
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.289 0.145 199.6
43: (ns/day) (hour/ns)
43: Performance: 5.364 4.474
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (633 ms)
43: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
43: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 3 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
43: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.431 0.216 199.8
43: (ns/day) (hour/ns)
43: Performance: 6.803 3.528
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.313 0.157 199.4
43: (ns/day) (hour/ns)
43: Performance: 4.961 4.838
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.445 0.223 199.8
43: (ns/day) (hour/ns)
43: Performance: 3.487 6.883
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (699 ms)
43: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
43: The Berendsen thermostat does not generate the correct kinetic energy
43: distribution. You might want to consider using the V-rescale thermostat.
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 3 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
43: The Berendsen thermostat does not generate the correct kinetic energy
43: distribution. You might want to consider using the V-rescale thermostat.
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.296 0.148 199.6
43: (ns/day) (hour/ns)
43: Performance: 9.893 2.426
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.446 0.223 199.6
43: (ns/day) (hour/ns)
43: Performance: 3.481 6.895
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.267 0.134 199.6
43: (ns/day) (hour/ns)
43: Performance: 5.815 4.127
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (589 ms)
43: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7
43: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (0 ms)
43: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/8
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.541 0.271 199.8
43: (ns/day) (hour/ns)
43: Performance: 5.420 4.428
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.401 0.201 199.5
43: (ns/day) (hour/ns)
43: Performance: 3.866 6.208
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.244 0.122 199.6
43: (ns/day) (hour/ns)
43: Performance: 6.349 3.780
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_secondpart.part0002.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/8 (677 ms)
43: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/9
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.477 0.239 199.9
43: (ns/day) (hour/ns)
43: Performance: 6.157 3.898
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.425 0.213 199.8
43: (ns/day) (hour/ns)
43: Performance: 3.656 6.564
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.491 0.245 199.9
43: (ns/day) (hour/ns)
43: Performance: 3.168 7.575
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_secondpart.part0002.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/9 (778 ms)
43: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/10
43: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/10 (0 ms)
43: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/11
43: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/11 (0 ms)
43: [----------] 12 tests from NPT/MdrunNoAppendContinuationIsExact (5857 ms total)
43:
43: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact
43: [ RUN ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.517 0.259 199.8
43: (ns/day) (hour/ns)
43: Performance: 5.672 4.231
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.491 0.246 199.6
43: (ns/day) (hour/ns)
43: Performance: 3.159 7.598
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.360 0.180 199.7
43: (ns/day) (hour/ns)
43: Performance: 4.316 5.561
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (776 ms)
43: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact (777 ms total)
43:
43: [----------] 3 tests from Checking/InitialConstraintsTest
43: [ RUN ] Checking/InitialConstraintsTest.Works/0
43: Setting the LD random seed to 1277211692
43: Generated 8 of the 10 non-bonded parameter combinations
43: Excluding 2 bonded neighbours molecule type 'Methanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group rest is 11.00
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]:
43: NVE simulation: will use the initial temperature of 1141.954 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc-and-methanol'
43: 1 steps, 0.0 ps.
43: turning H bonds into constraints...
43: turning H bonds into constraints...
43: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K
43: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.405 0.203 199.7
43: (ns/day) (hour/ns)
43: Performance: 0.852 28.170
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_spc-and-methanol.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/0 (239 ms)
43: [ RUN ] Checking/InitialConstraintsTest.Works/1
43: Setting the LD random seed to 1776257529
43: Generated 8 of the 10 non-bonded parameter combinations
43: Excluding 2 bonded neighbours molecule type 'Methanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group rest is 11.00
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]:
43: NVE simulation: will use the initial temperature of 1141.954 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc-and-methanol'
43: 1 steps, 0.0 ps.
43: turning H bonds into constraints...
43: turning H bonds into constraints...
43: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K
43: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.394 0.197 199.8
43: (ns/day) (hour/ns)
43: Performance: 0.877 27.359
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_spc-and-methanol.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/1 (234 ms)
43: [ RUN ] Checking/InitialConstraintsTest.Works/2
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]:
43: Integrator method md-vv-avek is implemented primarily for validation
43: purposes; for molecular dynamics, you should probably be using md or md-vv
43:
43: Setting the LD random seed to -1225073313
43: Generated 8 of the 10 non-bonded parameter combinations
43: Excluding 2 bonded neighbours molecule type 'Methanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group rest is 11.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]:
43: NVE simulation: will use the initial temperature of 1141.954 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc-and-methanol'
43: 1 steps, 0.0 ps.
43: turning H bonds into constraints...
43: turning H bonds into constraints...
43: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K
43: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.392 0.196 199.7
43: (ns/day) (hour/ns)
43: Performance: 0.881 27.253
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_spc-and-methanol.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/2 (233 ms)
43: [----------] 3 tests from Checking/InitialConstraintsTest (706 ms total)
43:
43: [----------] 2 tests from WithIntegrator/ImdTest
43: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/0
43: Setting the LD random seed to 915871638
43: Generated 20503 of the 20503 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 1
43: Generated 17396 of the 20503 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'Glycine'
43:
43: NOTE 1 [file glycine_vacuo.top, line 12]:
43: The bond in molecule-type Glycine between atoms 1 N and 2 H1 has an
43: estimated oscillational period of 1.0e-02 ps, which is less than 10 times
43: the time step of 2.0e-03 ps.
43: Maybe you forgot to change the constraints mdp option.
43:
43: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD).
43: Number of degrees of freedom in T-Coupling group System is 27.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 10 to 50, rlist from 1.026 to 1.34
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43:
43: IMD: Enabled. This simulation will accept incoming IMD connections.
43: IMD: Pulling from IMD remote is enabled (-imdpull).
43: IMD: Setting port for connection requests to 0.
43: IMD: Setting up incoming socket.
43: IMD: Listening for IMD connection on port 36879.
43: IMD: -imdwait not set, starting simulation.
43: starting mdrun 'Glycine'
43: 2 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
43: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.026 nm, buffer size 0.026 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.444 0.222 199.7
43: (ns/day) (hour/ns)
43: Performance: 2.331 10.296
43: [ OK ] WithIntegrator/ImdTest.ImdCanRun/0 (1289 ms)
43: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/1
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]:
43: Setting tcoupl from 'V-rescale' to 'no'. Temperature coupling does not
43: apply to steep.
43:
43: Setting the LD random seed to -125996393
43: Generated 20503 of the 20503 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 1
43: Generated 17396 of the 20503 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'Glycine'
43: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD).
43: Number of degrees of freedom in T-Coupling group System is 27.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43:
43: IMD: Enabled. This simulation will accept incoming IMD connections.
43: IMD: Pulling from IMD remote is enabled (-imdpull).
43: IMD: Setting port for connection requests to 0.
43: IMD: Setting up incoming socket.
43: IMD: Listening for IMD connection on port 46983.
43: IMD: -imdwait not set, starting simulation.
43:
43: Steepest Descents:
43: Tolerance (Fmax) = 1.00000e+01
43: Number of steps = 2
43:
43: Energy minimization reached the maximum number of steps before the forces
43: reached the requested precision Fmax < 10.
43:
43: writing lowest energy coordinates.
43:
43: Steepest Descents did not converge to Fmax < 10 in 3 steps.
43: Potential Energy = 1.1977063e+03
43: Maximum force = 1.7794877e+04 on atom 9
43: Norm of force = 7.8732901e+03
43: This run will generate roughly 0 Mb of data
43: [ OK ] WithIntegrator/ImdTest.ImdCanRun/1 (1044 ms)
43: [----------] 2 tests from WithIntegrator/ImdTest (2333 ms total)
43:
43: [----------] 2 tests from Argon12/OutputFiles
43: [ RUN ] Argon12/OutputFiles.FilesArePresent/0
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]:
43: NVE simulation: will use the initial temperature of 68.810 K for
43: determining the Verlet buffer size
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.620 0.310 199.8
43: (ns/day) (hour/ns)
43: Performance: 4.732 5.072
43: [ OK ] Argon12/OutputFiles.FilesArePresent/0 (346 ms)
43: [ RUN ] Argon12/OutputFiles.FilesArePresent/1
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]:
43: NVE simulation: will use the initial temperature of 68.810 K for
43: determining the Verlet buffer size
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.413 0.207 199.9
43: (ns/day) (hour/ns)
43: Performance: 7.112 3.375
43: [ OK ] Argon12/OutputFiles.FilesArePresent/1 (246 ms)
43: [----------] 2 tests from Argon12/OutputFiles (592 ms total)
43:
43: [----------] 3 tests from MdrunCanWrite/Trajectories
43: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0
43: Setting the LD random seed to 873448632
43: Generated 8 of the 10 non-bonded parameter combinations
43: Excluding 2 bonded neighbours molecule type 'Methanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 12.00
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There was 1 note
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc-and-methanol'
43: 6 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.288 0.144 199.6
43: (ns/day) (hour/ns)
43: Performance: 4.188 5.731
43: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 (226 ms)
43: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1
43: Setting the LD random seed to -833242974
43: Generated 8 of the 10 non-bonded parameter combinations
43: Excluding 2 bonded neighbours molecule type 'Methanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 12.00
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There was 1 note
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc-and-methanol'
43: 6 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.372 0.186 199.7
43: (ns/day) (hour/ns)
43: Performance: 3.248 7.389
43: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 (243 ms)
43: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2
43: Setting the LD random seed to -1428383201
43: Generated 8 of the 10 non-bonded parameter combinations
43: Excluding 2 bonded neighbours molecule type 'Methanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 12.00
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There was 1 note
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc-and-methanol'
43: 6 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.239 0.120 199.5
43: (ns/day) (hour/ns)
43: Performance: 5.058 4.745
43: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 (176 ms)
43: [----------] 3 tests from MdrunCanWrite/Trajectories (649 ms total)
43:
43: [----------] 3 tests from MdrunCanWrite/NptTrajectories
43: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0
43: Setting the LD random seed to -836840035
43: Generated 8 of the 10 non-bonded parameter combinations
43: Excluding 2 bonded neighbours molecule type 'Methanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 12.00
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There was 1 note
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc-and-methanol'
43: 2 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.394 0.197 199.7
43: (ns/day) (hour/ns)
43: Performance: 1.314 18.265
43: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 (252 ms)
43: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1
43: Setting the LD random seed to -1933112175
43: Generated 8 of the 10 non-bonded parameter combinations
43: Excluding 2 bonded neighbours molecule type 'Methanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 12.00
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There was 1 note
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc-and-methanol'
43: 2 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.221 0.111 199.4
43: (ns/day) (hour/ns)
43: Performance: 2.336 10.272
43: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 (160 ms)
43: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2
43: Setting the LD random seed to 1003368887
43: Generated 8 of the 10 non-bonded parameter combinations
43: Excluding 2 bonded neighbours molecule type 'Methanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 12.00
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There was 1 note
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
43: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc-and-methanol'
43: 2 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.208 0.104 199.4
43: (ns/day) (hour/ns)
43: Performance: 2.488 9.648
43: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 (145 ms)
43: [----------] 3 tests from MdrunCanWrite/NptTrajectories (560 ms total)
43:
43: [----------] Global test environment tear-down
43: [==========] 84 tests from 21 test cases ran. (87437 ms total)
43: [ PASSED ] 84 tests.
43:
43: YOU HAVE 12 DISABLED TESTS
43:
43/52 Test #43: MdrunTests .......................... Passed 87.53 sec
test 44
Start 44: MdrunNonIntegratorTests
44: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrun-non-integrator-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunNonIntegratorTests.xml"
44: Test timeout computed to be: 600
44: [==========] Running 58 tests from 5 test cases.
44: [----------] Global test environment set-up.
44: [----------] 1 test from NonbondedBenchTest
44: [ RUN ] NonbondedBenchTest.BasicEndToEndTest
44: System size: 3000 atoms
44: Cut-off radius: 1 nm
44: Number of threads: 1
44: Number of iterations: 1
44: Compute energies: no
44: Ewald excl. corr.: analytical
44:
44: Coulomb LJ comb. SIMD Mcycles Mcycles/it. pairs/cycle
44: total useful
44: Ewald all geom. no 0.000 0.0000 inf inf
44: [ OK ] NonbondedBenchTest.BasicEndToEndTest (526 ms)
44: [----------] 1 test from NonbondedBenchTest (526 ms total)
44:
44: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest
44: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
44: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
44: nstcomm to nstcalcenergy
44:
44: Generated 330891 of the 330891 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 330891 of the 330891 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 27.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44:
44: Steepest Descents:
44: Tolerance (Fmax) = 1.00000e+01
44: Number of steps = 4
44:
44: Energy minimization reached the maximum number of steps before the forces
44: reached the requested precision Fmax < 10.
44:
44: writing lowest energy coordinates.
44:
44: Steepest Descents did not converge to Fmax < 10 in 5 steps.
44: Potential Energy = -4.7990990e+01
44: Maximum force = 1.8629828e+02 on atom 13
44: Norm of force = 8.7721844e+01
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 This run will generate roughly 0 Mb of data
44: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (3153 ms)
44: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
44: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
44: nstcomm to nstcalcenergy
44:
44: Generated 330891 of the 330891 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 330891 of the 330891 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 27.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44:
44: Polak-Ribiere Conjugate Gradients:
44: Tolerance (Fmax) = 1.00000e+01
44: Number of steps = 4
44: F-max = 3.02331e+02 on atom 3
44: F-Norm = 1.18024e+02
44:
44:
44: Energy minimization reached the maximum number of steps before the forces
44: reached the requested precision Fmax < 10.
44:
44: writing lowest energy coordinates.
44:
44: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
44: Potential Energy = -5.5862099e+01
44: Maximum force = 4.2728845e+02 on atom 13
44: Norm of force = 1.8453478e+02
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data
44: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (3225 ms)
44: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
44: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
44: nstcomm to nstcalcenergy
44:
44: Generated 20503 of the 20503 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 1
44: Generated 17396 of the 20503 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Glycine'
44: Number of degrees of freedom in T-Coupling group System is 22.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44:
44: Steepest Descents:
44: Tolerance (Fmax) = 1.00000e+01
44: Number of steps = 4
44:
44: Energy minimization reached the maximum number of steps before the forces
44: reached the requested precision Fmax < 10.
44:
44: writing lowest energy coordinates.
44:
44: Steepest Descents did not converge to Fmax < 10 in 5 steps.
44: Potential Energy = 3.1937714e+02
44: Maximum force = 9.9988643e+03 on atom 9
44: Norm of force = 4.6166996e+03
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 turning H bonds into constraints...
44: This run will generate roughly 0 Mb of data
44: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (1080 ms)
44: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
44: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
44: nstcomm to nstcalcenergy
44:
44: Generated 20503 of the 20503 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 1
44: Generated 17396 of the 20503 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Glycine'
44:
44: NOTE 3 [file glycine_vacuo.top, line 12]:
44: For accurate cg with LINCS constraints, lincs-order should be 8 or more.
44:
44: Number of degrees of freedom in T-Coupling group System is 22.00
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44:
44: Polak-Ribiere Conjugate Gradients:
44: Tolerance (Fmax) = 1.00000e+01
44: Number of steps = 4
44: F-max = 2.41575e+04 on atom 10
44: F-Norm = 1.18451e+04
44:
44:
44: Energy minimization reached the maximum number of steps before the forces
44: reached the requested precision Fmax < 10.
44:
44: writing lowest energy coordinates.
44:
44: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
44: Potential Energy = 1.5174377e+02
44: Maximum force = 7.4208838e+03 on atom 9
44: Norm of force = 3.5693005e+03
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 turning H bonds into constraints...
44: This run will generate roughly 0 Mb of data
44: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (1041 ms)
44: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
44: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
44: nstcomm to nstcalcenergy
44:
44: Generated 2145 of the 2145 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2145 of the 2145 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
44:
44: NOTE 3 [file unknown]:
44: You are using constraints on all bonds, whereas the forcefield has been
44: parametrized only with constraints involving hydrogen atoms. We suggest
44: using constraints = h-bonds instead, this will also improve performance.
44:
44: Cleaning up constraints and constant bonded interactions with virtual sites
44: Removed 18 Angles with virtual sites, 21 left
44: Removed 10 Proper Dih.s with virtual sites, 44 left
44: Converted 15 Constraints with virtual sites to connections, 7 left
44: Number of degrees of freedom in T-Coupling group System is 23.00
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44:
44: Steepest Descents:
44: Tolerance (Fmax) = 1.00000e+01
44: Number of steps = 4
44:
44: Energy minimization reached the maximum number of steps before the forces
44: reached the requested precision Fmax < 10.
44:
44: writing lowest energy coordinates.
44:
44: Steepest Descents did not converge to Fmax < 10 in 5 steps.
44: Potential Energy = -1.5698413e+02
44: Maximum force = 4.5704984e+02 on atom 17
44: Norm of force = 1.8327747e+02
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 3.000
Last energy frame read 2 time 3.000 turning all bonds into constraints...
44: This run will generate roughly 0 Mb of data
44: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (115 ms)
44: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
44: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
44: nstcomm to nstcalcenergy
44:
44: Generated 2145 of the 2145 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2145 of the 2145 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
44:
44: NOTE 3 [file unknown]:
44: You are using constraints on all bonds, whereas the forcefield has been
44: parametrized only with constraints involving hydrogen atoms. We suggest
44: using constraints = h-bonds instead, this will also improve performance.
44:
44:
44: NOTE 4 [file unknown]:
44: For accurate cg with LINCS constraints, lincs-order should be 8 or more.
44:
44: Cleaning up constraints and constant bonded interactions with virtual sites
44: Removed 18 Angles with virtual sites, 21 left
44: Removed 10 Proper Dih.s with virtual sites, 44 left
44: Converted 15 Constraints with virtual sites to connections, 7 left
44: Number of degrees of freedom in T-Coupling group System is 23.00
44:
44: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 5 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44:
44: Polak-Ribiere Conjugate Gradients:
44: Tolerance (Fmax) = 1.00000e+01
44: Number of steps = 4
44: F-max = 1.06801e+03 on atom 28
44: F-Norm = 4.26916e+02
44:
44:
44: Energy minimization reached the maximum number of steps before the forces
44: reached the requested precision Fmax < 10.
44:
44: writing lowest energy coordinates.
44:
44: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
44: Potential Energy = -1.6941180e+02
44: Maximum force = 2.1832491e+02 on atom 17
44: Norm of force = 7.9220732e+01
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 turning all bonds into constraints...
44: This run will generate roughly 0 Mb of data
44: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (116 ms)
44: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (8731 ms total)
44:
44: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest
44: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
44: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
44: nstcomm to nstcalcenergy
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44:
44: Steepest Descents:
44: Tolerance (Fmax) = 1.00000e+01
44: Number of steps = 4
44:
44: writing lowest energy coordinates.
44:
44: Steepest Descents converged to Fmax < 10 in 1 steps
44: Potential Energy = -9.7425699e-01
44: Maximum force = 4.0132303e+00 on atom 1
44: Norm of force = 1.6383944e+00
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
44: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (35 ms)
44: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
44: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
44: nstcomm to nstcalcenergy
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44:
44: Polak-Ribiere Conjugate Gradients:
44: Tolerance (Fmax) = 1.00000e+01
44: Number of steps = 4
44: F-max = 4.01323e+00 on atom 1
44: F-Norm = 1.63839e+00
44:
44:
44: writing lowest energy coordinates.
44:
44: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps
44: Potential Energy = -9.9064207e-01
44: Maximum force = 2.5781622e+00 on atom 1
44: Norm of force = 1.0525302e+00
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Last energy frame read 1 time 0.000 This run will generate roughly 0 Mb of data
44: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (36 ms)
44: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
44: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
44: nstcomm to nstcalcenergy
44:
44:
44: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
44: For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44:
44: There was 1 warning
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank.
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44:
44: Low-Memory BFGS Minimizer:
44: Tolerance (Fmax) = 1.00000e+01
44: Number of steps = 4
44: Using 10 BFGS correction steps.
44:
44: F-max = 4.01323e+00 on atom 1
44: F-Norm = 1.63839e+00
44:
44:
44: writing lowest energy coordinates.
44:
44: Low-Memory BFGS Minimizer converged to Fmax < 10 in 0 steps
44: Potential Energy = -9.9064207e-01
44: Maximum force = 2.5781622e+00 on atom 1
44: Norm of force = 1.0525302e+00
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Last energy frame read 1 time 0.000 This run will generate roughly 0 Mb of data
44: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (36 ms)
44: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
44: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
44: nstcomm to nstcalcenergy
44:
44: Generated 20503 of the 20503 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 1
44: Generated 17396 of the 20503 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Glycine'
44: Number of degrees of freedom in T-Coupling group System is 27.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44:
44: Steepest Descents:
44: Tolerance (Fmax) = 1.00000e+01
44: Number of steps = 4
44:
44: Energy minimization reached the maximum number of steps before the forces
44: reached the requested precision Fmax < 10.
44:
44: writing lowest energy coordinates.
44:
44: Steepest Descents did not converge to Fmax < 10 in 5 steps.
44: Potential Energy = 3.1939697e+02
44: Maximum force = 9.9704248e+03 on atom 9
44: Norm of force = 4.6227540e+03
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 This run will generate roughly 0 Mb of data
44: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (1035 ms)
44: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
44: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
44: nstcomm to nstcalcenergy
44:
44: Generated 20503 of the 20503 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 1
44: Generated 17396 of the 20503 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Glycine'
44: Number of degrees of freedom in T-Coupling group System is 27.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44:
44: Polak-Ribiere Conjugate Gradients:
44: Tolerance (Fmax) = 1.00000e+01
44: Number of steps = 4
44: F-max = 2.41672e+04 on atom 10
44: F-Norm = 1.19357e+04
44:
44:
44: Energy minimization reached the maximum number of steps before the forces
44: reached the requested precision Fmax < 10.
44:
44: writing lowest energy coordinates.
44:
44: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
44: Potential Energy = 1.5625757e+02
44: Maximum force = 7.5018242e+03 on atom 9
44: Norm of force = 3.6139019e+03
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data
44: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (1035 ms)
44: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
44: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
44: nstcomm to nstcalcenergy
44:
44:
44: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
44: For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
44:
44: Generated 20503 of the 20503 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 1
44: Generated 17396 of the 20503 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Glycine'
44: Number of degrees of freedom in T-Coupling group System is 27.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44:
44: There was 1 warning
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank.
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44:
44: Low-Memory BFGS Minimizer:
44: Tolerance (Fmax) = 1.00000e+01
44: Number of steps = 4
44: Using 10 BFGS correction steps.
44:
44: F-max = 2.41672e+04 on atom 10
44: F-Norm = 1.19357e+04
44:
44:
44: Energy minimization reached the maximum number of steps before the forces
44: reached the requested precision Fmax < 10.
44:
44: writing lowest energy coordinates.
44:
44: Low-Memory BFGS Minimizer did not converge to Fmax < 10 in 5 steps.
44: Potential Energy = 5.6111725e+02
44: Maximum force = 1.2685491e+04 on atom 10
44: Norm of force = 6.0643622e+03
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data
44: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (1045 ms)
44: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (3223 ms total)
44:
44: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest
44: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]:
44: NVE simulation: will use the initial temperature of 68.810 K for
44: determining the Verlet buffer size
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.512 0.256 199.8
44: (ns/day) (hour/ns)
44: Performance: 5.735 4.185
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun 'Argon', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.trr'
44:
44: trr version: GMX_trn_file (single precision)
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.006 0.003 192.7
44: (ns/day) (hour/ns)
44: Performance: 502.209 0.048
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 (309 ms)
44: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]:
44: NVE simulation: will use the initial temperature of 68.810 K for
44: determining the Verlet buffer size
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.471 0.236 199.8
44: (ns/day) (hour/ns)
44: Performance: 6.225 3.855
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun 'Argon', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.006 0.003 192.6
44: (ns/day) (hour/ns)
44: Performance: 509.561 0.047
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 (289 ms)
44: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.708 nm, buffer size 0.008 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.708 nm, buffer size 0.008 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.402 0.201 199.8
44: (ns/day) (hour/ns)
44: Performance: 7.304 3.286
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun 'Argon', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.006 0.003 192.5
44: (ns/day) (hour/ns)
44: Performance: 498.995 0.048
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 (256 ms)
44: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.335 0.168 199.7
44: (ns/day) (hour/ns)
44: Performance: 8.747 2.744
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun 'Argon', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.006 0.003 192.8
44: (ns/day) (hour/ns)
44: Performance: 490.571 0.049
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 (222 ms)
44: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 330891 of the 330891 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 330891 of the 330891 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 27.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]:
44: NVE simulation: will use the initial temperature of 398.997 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
44: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.539 0.270 199.8
44: (ns/day) (hour/ns)
44: Performance: 5.442 4.410
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun 'spc2', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.008 0.004 194.1
44: (ns/day) (hour/ns)
44: Performance: 366.092 0.066
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 (3508 ms)
44: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 330891 of the 330891 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 330891 of the 330891 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 27.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]:
44: NVE simulation: will use the initial temperature of 398.997 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
44: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.478 0.239 199.8
44: (ns/day) (hour/ns)
44: Performance: 6.145 3.906
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun 'spc2', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.006 0.003 192.5
44: (ns/day) (hour/ns)
44: Performance: 465.759 0.052
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 (3453 ms)
44: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 330891 of the 330891 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 330891 of the 330891 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 27.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.733 to 0.824
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.735 nm, buffer size 0.035 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.733 nm, buffer size 0.033 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.454 0.227 199.8
44: (ns/day) (hour/ns)
44: Performance: 6.463 3.714
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.733 to 0.824
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun 'spc2', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.006 0.003 193.0
44: (ns/day) (hour/ns)
44: Performance: 442.190 0.054
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 (3433 ms)
44: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 330891 of the 330891 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 330891 of the 330891 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 27.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.342 0.171 199.7
44: (ns/day) (hour/ns)
44: Performance: 8.584 2.796
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun 'spc2', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.007 0.003 193.0
44: (ns/day) (hour/ns)
44: Performance: 428.206 0.056
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 (3393 ms)
44: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2145 of the 2145 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2145 of the 2145 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
44:
44: NOTE 3 [file unknown]:
44: You are using constraints on all bonds, whereas the forcefield has been
44: parametrized only with constraints involving hydrogen atoms. We suggest
44: using constraints = h-bonds instead, this will also improve performance.
44:
44: Cleaning up constraints and constant bonded interactions with virtual sites
44: Removed 18 Angles with virtual sites, 21 left
44: Removed 10 Proper Dih.s with virtual sites, 44 left
44: Converted 15 Constraints with virtual sites to connections, 7 left
44: Number of degrees of freedom in T-Coupling group System is 23.00
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
44: NVE simulation: will use the initial temperature of 456.887 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
44: There are 9 non-linear virtual site constructions. Their contribution to
44: the energy error is approximated. In most cases this does not affect the
44: error significantly.
44:
44:
44: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 6 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 16 steps, 0.0 ps.
44: turning all bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
44: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.500 0.250 199.7
44: (ns/day) (hour/ns)
44: Performance: 5.871 4.088
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.011 0.005 194.3
44: (ns/day) (hour/ns)
44: Performance: 271.727 0.088
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 (402 ms)
44: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2145 of the 2145 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2145 of the 2145 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
44:
44: NOTE 3 [file unknown]:
44: You are using constraints on all bonds, whereas the forcefield has been
44: parametrized only with constraints involving hydrogen atoms. We suggest
44: using constraints = h-bonds instead, this will also improve performance.
44:
44: Cleaning up constraints and constant bonded interactions with virtual sites
44: Removed 18 Angles with virtual sites, 21 left
44: Removed 10 Proper Dih.s with virtual sites, 44 left
44: Converted 15 Constraints with virtual sites to connections, 7 left
44: Number of degrees of freedom in T-Coupling group System is 23.00
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
44: NVE simulation: will use the initial temperature of 456.887 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
44: There are 9 non-linear virtual site constructions. Their contribution to
44: the energy error is approximated. In most cases this does not affect the
44: error significantly.
44:
44:
44: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 6 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 16 steps, 0.0 ps.
44: turning all bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
44: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.521 0.261 199.7
44: (ns/day) (hour/ns)
44: Performance: 5.629 4.264
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.010 0.005 193.9
44: (ns/day) (hour/ns)
44: Performance: 272.352 0.088
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 (411 ms)
44: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2145 of the 2145 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2145 of the 2145 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
44:
44: NOTE 3 [file unknown]:
44: You are using constraints on all bonds, whereas the forcefield has been
44: parametrized only with constraints involving hydrogen atoms. We suggest
44: using constraints = h-bonds instead, this will also improve performance.
44:
44: Cleaning up constraints and constant bonded interactions with virtual sites
44: Removed 18 Angles with virtual sites, 21 left
44: Removed 10 Proper Dih.s with virtual sites, 44 left
44: Converted 15 Constraints with virtual sites to connections, 7 left
44: Number of degrees of freedom in T-Coupling group System is 23.00
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]:
44: There are 9 non-linear virtual site constructions. Their contribution to
44: the energy error is approximated. In most cases this does not affect the
44: error significantly.
44:
44:
44: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 5 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 16 steps, 0.0 ps.
44: turning all bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.748 nm, buffer size 0.048 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.744 nm, buffer size 0.044 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.495 0.248 199.7
44: (ns/day) (hour/ns)
44: Performance: 5.922 4.053
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.011 0.006 192.6
44: (ns/day) (hour/ns)
44: Performance: 262.108 0.092
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 (513 ms)
44: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2145 of the 2145 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2145 of the 2145 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
44:
44: NOTE 3 [file unknown]:
44: You are using constraints on all bonds, whereas the forcefield has been
44: parametrized only with constraints involving hydrogen atoms. We suggest
44: using constraints = h-bonds instead, this will also improve performance.
44:
44: Cleaning up constraints and constant bonded interactions with virtual sites
44: Removed 18 Angles with virtual sites, 21 left
44: Removed 10 Proper Dih.s with virtual sites, 44 left
44: Converted 15 Constraints with virtual sites to connections, 7 left
44: Number of degrees of freedom in T-Coupling group System is 23.00
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]:
44: There are 9 non-linear virtual site constructions. Their contribution to
44: the energy error is approximated. In most cases this does not affect the
44: error significantly.
44:
44:
44: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 5 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 16 steps, 0.0 ps.
44: turning all bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.555 0.278 199.7
44: (ns/day) (hour/ns)
44: Performance: 5.286 4.540
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.011 0.006 194.3
44: (ns/day) (hour/ns)
44: Performance: 266.323 0.090
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 (503 ms)
44: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest (16693 ms total)
44:
44: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.591 0.296 199.7
44: (ns/day) (hour/ns)
44: Performance: 4.960 4.839
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.014 0.007 185.8
44: (ns/day) (hour/ns)
44: Performance: 198.300 0.121
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 (445 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.592 0.296 199.7
44: (ns/day) (hour/ns)
44: Performance: 4.956 4.842
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.014 0.007 184.3
44: (ns/day) (hour/ns)
44: Performance: 200.052 0.120
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 (444 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.643 0.322 199.7
44: (ns/day) (hour/ns)
44: Performance: 4.561 5.263
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.014 0.007 187.1
44: (ns/day) (hour/ns)
44: Performance: 200.599 0.120
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 (478 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.545 0.273 199.7
44: (ns/day) (hour/ns)
44: Performance: 5.379 4.462
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.014 0.007 185.9
44: (ns/day) (hour/ns)
44: Performance: 199.870 0.120
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 (422 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.391 0.196 199.6
44: (ns/day) (hour/ns)
44: Performance: 7.495 3.202
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.014 0.007 186.9
44: (ns/day) (hour/ns)
44: Performance: 200.906 0.119
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 (345 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.365 0.183 199.5
44: (ns/day) (hour/ns)
44: Performance: 8.026 2.990
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.014 0.007 187.1
44: (ns/day) (hour/ns)
44: Performance: 199.404 0.120
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 (333 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.612 0.306 199.7
44: (ns/day) (hour/ns)
44: Performance: 4.794 5.007
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.015 0.008 187.9
44: (ns/day) (hour/ns)
44: Performance: 186.741 0.129
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 (461 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.548 0.275 199.7
44: (ns/day) (hour/ns)
44: Performance: 5.349 4.487
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.015 0.008 186.6
44: (ns/day) (hour/ns)
44: Performance: 187.634 0.128
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 (432 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.550 0.276 199.7
44: (ns/day) (hour/ns)
44: Performance: 5.330 4.503
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.015 0.008 187.9
44: (ns/day) (hour/ns)
44: Performance: 189.027 0.127
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 (433 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.638 0.319 199.7
44: (ns/day) (hour/ns)
44: Performance: 4.598 5.220
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.015 0.008 187.6
44: (ns/day) (hour/ns)
44: Performance: 186.476 0.129
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 (478 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.550 0.275 199.7
44: (ns/day) (hour/ns)
44: Performance: 5.334 4.499
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.015 0.008 187.6
44: (ns/day) (hour/ns)
44: Performance: 188.697 0.127
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 (433 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.577 0.289 199.9
44: (ns/day) (hour/ns)
44: Performance: 5.086 4.719
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.015 0.008 186.8
44: (ns/day) (hour/ns)
44: Performance: 187.081 0.128
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 (445 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.420 0.210 199.8
44: (ns/day) (hour/ns)
44: Performance: 6.995 3.431
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.015 0.008 187.8
44: (ns/day) (hour/ns)
44: Performance: 187.588 0.128
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 (366 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.398 0.199 199.8
44: (ns/day) (hour/ns)
44: Performance: 7.370 3.257
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.015 0.008 187.8
44: (ns/day) (hour/ns)
44: Performance: 187.955 0.128
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 (355 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.598 0.299 199.9
44: (ns/day) (hour/ns)
44: Performance: 4.908 4.890
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.014 0.008 187.6
44: (ns/day) (hour/ns)
44: Performance: 190.365 0.126
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 (455 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.640 0.320 199.9
44: (ns/day) (hour/ns)
44: Performance: 4.586 5.233
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.014 0.007 186.8
44: (ns/day) (hour/ns)
44: Performance: 201.584 0.119
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 (472 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.612 0.306 199.9
44: (ns/day) (hour/ns)
44: Performance: 4.801 4.999
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.014 0.007 187.0
44: (ns/day) (hour/ns)
44: Performance: 197.963 0.121
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 (456 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.588 0.294 199.9
44: (ns/day) (hour/ns)
44: Performance: 4.989 4.811
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.014 0.007 186.9
44: (ns/day) (hour/ns)
44: Performance: 199.708 0.120
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 (445 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.543 0.272 199.9
44: (ns/day) (hour/ns)
44: Performance: 5.407 4.439
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.014 0.007 186.0
44: (ns/day) (hour/ns)
44: Performance: 199.721 0.120
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 (422 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.493 0.247 199.8
44: (ns/day) (hour/ns)
44: Performance: 5.949 4.034
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.014 0.007 187.1
44: (ns/day) (hour/ns)
44: Performance: 203.239 0.118
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 (400 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.633 0.317 199.9
44: (ns/day) (hour/ns)
44: Performance: 4.639 5.173
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.018 0.009 187.7
44: (ns/day) (hour/ns)
44: Performance: 157.222 0.153
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 (485 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.932 0.466 199.9
44: (ns/day) (hour/ns)
44: Performance: 3.149 7.620
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.014 0.007 187.2
44: (ns/day) (hour/ns)
44: Performance: 199.449 0.120
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 (626 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.614 0.307 199.7
44: (ns/day) (hour/ns)
44: Performance: 4.777 5.024
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.014 0.007 187.5
44: (ns/day) (hour/ns)
44: Performance: 196.510 0.122
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 (541 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.467 0.234 199.6
44: (ns/day) (hour/ns)
44: Performance: 6.277 3.823
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.014 0.007 187.3
44: (ns/day) (hour/ns)
44: Performance: 199.721 0.120
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 (466 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.512 0.256 199.7
44: (ns/day) (hour/ns)
44: Performance: 5.732 4.187
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.014 0.007 187.2
44: (ns/day) (hour/ns)
44: Performance: 197.639 0.121
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 (490 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.466 0.233 199.6
44: (ns/day) (hour/ns)
44: Performance: 6.291 3.815
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.014 0.007 186.8
44: (ns/day) (hour/ns)
44: Performance: 198.754 0.121
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 (466 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.600 0.300 199.7
44: (ns/day) (hour/ns)
44: Performance: 4.890 4.908
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.014 0.007 187.2
44: (ns/day) (hour/ns)
44: Performance: 199.592 0.120
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 (533 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.646 0.323 199.7
44: (ns/day) (hour/ns)
44: Performance: 4.542 5.284
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.014 0.007 187.0
44: (ns/day) (hour/ns)
44: Performance: 198.268 0.121
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 (556 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.650 0.326 199.7
44: (ns/day) (hour/ns)
44: Performance: 4.511 5.320
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.015 0.008 189.6
44: (ns/day) (hour/ns)
44: Performance: 179.745 0.134
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 (576 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.595 0.298 199.7
44: (ns/day) (hour/ns)
44: Performance: 4.929 4.869
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.014 0.007 187.1
44: (ns/day) (hour/ns)
44: Performance: 198.122 0.121
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 (534 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.597 0.299 199.7
44: (ns/day) (hour/ns)
44: Performance: 4.910 4.888
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.014 0.007 187.2
44: (ns/day) (hour/ns)
44: Performance: 199.721 0.120
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 (533 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.577 0.289 199.7
44: (ns/day) (hour/ns)
44: Performance: 5.083 4.721
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.014 0.007 186.7
44: (ns/day) (hour/ns)
44: Performance: 196.749 0.122
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 (522 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.598 0.300 199.7
44: (ns/day) (hour/ns)
44: Performance: 4.901 4.897
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.014 0.007 187.1
44: (ns/day) (hour/ns)
44: Performance: 200.371 0.120
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim2.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 (533 ms)
44: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest (15387 ms total)
44:
44: [----------] Global test environment tear-down
44: [==========] 58 tests from 5 test cases ran. (44561 ms total)
44: [ PASSED ] 58 tests.
44/52 Test #44: MdrunNonIntegratorTests ............. Passed 44.65 sec
test 45
Start 45: MdrunTpiTests
45: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrun-tpi-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunTpiTests.xml"
45: Test timeout computed to be: 600
45: [==========] Running 2 tests from 1 test case.
45: [----------] Global test environment set-up.
45: [----------] 2 tests from Simple/TpiTest
45: [ RUN ] Simple/TpiTest.ReproducesOutput/0
45: Ignoring obsolete mdp entry 'ns_type'
45: Generated 331705 of the 331705 non-bonded parameter combinations
45: Generating 1-4 interactions: fudge = 0.5
45: Generated 331705 of the 331705 1-4 parameter combinations
45: Excluding 2 bonded neighbours molecule type 'SOL'
45: Excluding 3 bonded neighbours molecule type 'methane'
45: Number of degrees of freedom in T-Coupling group System is 1308.00
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
45: TPI is not implemented for GPUs.
45:
45: Using 1 MPI thread
45: Using 1 OpenMP thread
45:
45:
45: NOTE: Thread affinity was not set.
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: Reading frames from gro file '216 water molecules', 648 atoms.
45:
Reading frame 0 time 0.000 mu 8.706e+02 <mu> 8.706e+02
45:
Last frame 0 time 0.000
45: Analysing residue names:
45: There are: 216 Water residues
45: There are: 1 Other residues
45: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
45: This run will generate roughly 0 Mb of data
45: [ OK ] Simple/TpiTest.ReproducesOutput/0 (3533 ms)
45: [ RUN ] Simple/TpiTest.ReproducesOutput/1
45: Ignoring obsolete mdp entry 'ns_type'
45: Generated 331705 of the 331705 non-bonded parameter combinations
45: Generating 1-4 interactions: fudge = 0.5
45: Generated 331705 of the 331705 1-4 parameter combinations
45: Excluding 2 bonded neighbours molecule type 'SOL'
45: Excluding 3 bonded neighbours molecule type 'methane'
45: Number of degrees of freedom in T-Coupling group System is 1308.00
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_1.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
45: TPI is not implemented for GPUs.
45:
45: Using 1 MPI thread
45: Using 1 OpenMP thread
45:
45:
45: NOTE: Thread affinity was not set.
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: Reading frames from gro file '216 water molecules', 648 atoms.
45:
Reading frame 0 time 0.000 mu 9.144e+01 <mu> 9.144e+01
45:
Last frame 0 time 0.000
45: Analysing residue names:
45: There are: 216 Water residues
45: There are: 1 Other residues
45: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
45: This run will generate roughly 0 Mb of data
45: [ OK ] Simple/TpiTest.ReproducesOutput/1 (3555 ms)
45: [----------] 2 tests from Simple/TpiTest (7089 ms total)
45:
45: [----------] Global test environment tear-down
45: [==========] 2 tests from 1 test case ran. (7089 ms total)
45: [ PASSED ] 2 tests.
45/52 Test #45: MdrunTpiTests ....................... Passed 7.16 sec
test 46
Start 46: MdrunMpiTests
46: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrun-mpi-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunMpiTests.xml"
46: Test timeout computed to be: 600
46: [==========] Running 22 tests from 7 test cases.
46: [----------] Global test environment set-up.
46: [----------] 1 test from DomainDecompositionSpecialCasesTest
46: [ RUN ] DomainDecompositionSpecialCasesTest.AnEmptyDomainWorks
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]:
46: For a correct single-point energy evaluation with nsteps = 0, use
46: continuation = yes to avoid constraining the input coordinates.
46:
46: Setting the LD random seed to 755521115
46: Generated 3 of the 3 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 3 of the 3 1-4 parameter combinations
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group rest is 9.00
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]:
46: NVE simulation with an initial temperature of zero: will use a Verlet
46: buffer of 10%. Check your energy drift!
46:
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 2 MPI threads
46: Using 2 OpenMP threads per tMPI thread
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'spc2'
46: 0 steps, 0.0 ps.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.005 0.002 312.6
46: (ns/day) (hour/ns)
46: Performance: 50.698 0.473
46: This run will generate roughly 0 Mb of data
46: [ OK ] DomainDecompositionSpecialCasesTest.AnEmptyDomainWorks (85 ms)
46: [----------] 1 test from DomainDecompositionSpecialCasesTest (85 ms total)
46:
46: [----------] 4 tests from MimicTest
46: [ RUN ] MimicTest.OneQuantumMol
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
46: For a correct single-point energy evaluation with nsteps = 0, use
46: continuation = yes to avoid constraining the input coordinates.
46:
46: Setting the LD random seed to -27664419
46: Generated 10 of the 10 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 10 of the 10 1-4 parameter combinations
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group rest is 21.00
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
46: NVE simulation with an initial temperature of zero: will use a Verlet
46: buffer of 10%. Check your energy drift!
46:
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 2 MPI threads
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads per tMPI thread
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
46:
46: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
46:
Reading frame 0 time 0.000
Last frame 0 time 0.000
46:
46: Core t (s) Wall t (s) (%)
46: Time: 2.649 0.692 382.7
46: (ns/day) (hour/ns)
46: Performance: 0.125 192.304
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
46: [ OK ] MimicTest.OneQuantumMol (2110 ms)
46: [ RUN ] MimicTest.AllQuantumMol
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
46: For a correct single-point energy evaluation with nsteps = 0, use
46: continuation = yes to avoid constraining the input coordinates.
46:
46: Setting the LD random seed to -208764580
46: Generated 10 of the 10 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 10 of the 10 1-4 parameter combinations
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group rest is 21.00
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
46: NVE simulation with an initial temperature of zero: will use a Verlet
46: buffer of 10%. Check your energy drift!
46:
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 2 MPI threads
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads per tMPI thread
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
46:
46: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
46:
Reading frame 0 time 0.000
Last frame 0 time 0.000
46:
46: Core t (s) Wall t (s) (%)
46: Time: 2.669 0.697 382.8
46: (ns/day) (hour/ns)
46: Performance: 0.124 193.671
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
46: [ OK ] MimicTest.AllQuantumMol (2109 ms)
46: [ RUN ] MimicTest.TwoQuantumMol
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
46: For a correct single-point energy evaluation with nsteps = 0, use
46: continuation = yes to avoid constraining the input coordinates.
46:
46: Setting the LD random seed to 1589577135
46: Generated 10 of the 10 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 10 of the 10 1-4 parameter combinations
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group rest is 21.00
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
46: NVE simulation with an initial temperature of zero: will use a Verlet
46: buffer of 10%. Check your energy drift!
46:
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 2 MPI threads
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads per tMPI thread
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
46:
46: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
46:
Reading frame 0 time 0.000
Last frame 0 time 0.000
46:
46: Core t (s) Wall t (s) (%)
46: Time: 2.570 0.672 382.2
46: (ns/day) (hour/ns)
46: Performance: 0.128 186.773
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
46: [ OK ] MimicTest.TwoQuantumMol (2062 ms)
46: [ RUN ] MimicTest.BondCuts
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
46: For a correct single-point energy evaluation with nsteps = 0, use
46: continuation = yes to avoid constraining the input coordinates.
46:
46: Setting the LD random seed to -468650006
46: Generated 2211 of the 2211 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2211 of the 2211 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
46: Number of degrees of freedom in T-Coupling group rest is 66.00
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
46: NVE simulation: will use the initial temperature of 300.368 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 2 MPI threads
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads per tMPI thread
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/ala.gro'
46:
46: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms.
46:
Reading frame 0 time 0.000
Last frame 0 time 0.000
46:
46: Core t (s) Wall t (s) (%)
46: Time: 2.509 0.657 381.7
46: (ns/day) (hour/ns)
46: Performance: 0.131 182.582
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K
46: Calculated rlist for 1x1 atom pair-list as 1.034 nm, buffer size 0.034 nm
46: Set rlist, assuming 4x4 atom pair-list, to 1.025 nm, buffer size 0.025 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46: [ OK ] MimicTest.BondCuts (2086 ms)
46: [----------] 4 tests from MimicTest (8370 ms total)
46:
46: [----------] 1 test from MultiSimTerminationTest
46: [ RUN ] MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts
46: [ OK ] MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (0 ms)
46: [----------] 1 test from MultiSimTerminationTest (0 ms total)
46:
46: [----------] 3 tests from PmeTest
46: [ RUN ] PmeTest.ReproducesEnergies
46: Setting the LD random seed to 276671034
46: Generated 8 of the 10 non-bonded parameter combinations
46: Excluding 2 bonded neighbours molecule type 'Methanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group rest is 12.00
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
46: NVE simulation: will use the initial temperature of 1046.791 K for
46: determining the Verlet buffer size
46:
46: Estimate for the relative computational load of the PME mesh part: 1.00
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
46: The optimal PME mesh load for parallel simulations is below 0.5
46: and for highly parallel simulations between 0.25 and 0.33,
46: for higher performance, increase the cut-off and the PME grid spacing.
46:
46:
46:
46: There were 2 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 2 MPI threads
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads per tMPI thread
46: Using 0 OpenMP thread per tMPI thread for PME
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'spc-and-methanol'
46: 20 steps, 0.0 ps.
46: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
46: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
46: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: Calculating fourier grid dimensions for X Y Z
46: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 8.357 2.127 392.9
46: (ns/day) (hour/ns)
46: Performance: 0.853 28.137
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeAuto.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 2 MPI threads
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads per tMPI thread
46: Using 0 OpenMP thread per tMPI thread for PME
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'spc-and-methanol'
46: 20 steps, 0.0 ps.
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 8.147 2.075 392.7
46: (ns/day) (hour/ns)
46: Performance: 0.875 27.444
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpu.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 2 MPI threads
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads per tMPI thread
46: Using 0 OpenMP thread per tMPI thread for PME
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
46: starting mdrun 'spc-and-methanol'
46: 20 steps, 0.0 ps.
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 8.125 2.070 392.6
46: (ns/day) (hour/ns)
46: Performance: 0.877 27.377
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpuTune.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 [ OK ] PmeTest.ReproducesEnergies (29210 ms)
46: [ RUN ] PmeTest.ScalesTheBox
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
46: For a correct single-point energy evaluation with nsteps = 0, use
46: continuation = yes to avoid constraining the input coordinates.
46:
46: Setting the LD random seed to 828611645
46: Generated 8 of the 10 non-bonded parameter combinations
46: Excluding 2 bonded neighbours molecule type 'Methanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group rest is 12.00
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
46: NVE simulation: will use the initial temperature of 1046.791 K for
46: determining the Verlet buffer size
46:
46: Estimate for the relative computational load of the PME mesh part: 1.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
46: The optimal PME mesh load for parallel simulations is below 0.5
46: and for highly parallel simulations between 0.25 and 0.33,
46: for higher performance, increase the cut-off and the PME grid spacing.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 2 MPI threads
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads per tMPI thread
46: Using 0 OpenMP thread per tMPI thread for PME
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'spc-and-methanol'
46: 0 steps, 0.0 ps.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.370 0.135 274.8
46: (ns/day) (hour/ns)
46: Performance: 0.641 37.442
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_spc-and-methanol_PmeOnCpu.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
46: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
46: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: Calculating fourier grid dimensions for X Y Z
46: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108
46: This run will generate roughly 0 Mb of data
46: [ OK ] PmeTest.ScalesTheBox (1083 ms)
46: [ RUN ] PmeTest.ScalesTheBoxWithWalls
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
46: For a correct single-point energy evaluation with nsteps = 0, use
46: continuation = yes to avoid constraining the input coordinates.
46:
46: Setting the LD random seed to -819481170
46: Generated 8 of the 10 non-bonded parameter combinations
46: Excluding 2 bonded neighbours molecule type 'Methanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Searching the wall atom type(s)
46: Number of degrees of freedom in T-Coupling group rest is 13.00
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
46: NVE simulation: will use the initial temperature of 966.268 K for
46: determining the Verlet buffer size
46:
46: Estimate for the relative computational load of the PME mesh part: 1.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
46: The optimal PME mesh load for parallel simulations is below 0.5
46: and for highly parallel simulations between 0.25 and 0.33,
46: for higher performance, increase the cut-off and the PME grid spacing.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 2 MPI threads
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads per tMPI thread
46: Using 0 OpenMP thread per tMPI thread for PME
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'spc-and-methanol'
46: 0 steps, 0.0 ps.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.585 0.187 312.1
46: (ns/day) (hour/ns)
46: Performance: 0.461 52.028
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_spc-and-methanol_PmeOnCpu.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K
46: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
46: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: Calculating fourier grid dimensions for X Y Z
46: Using a fourier grid of 28x28x128, spacing 0.108 0.108 0.118
46: This run will generate roughly 0 Mb of data
46: [ OK ] PmeTest.ScalesTheBoxWithWalls (63634 ms)
46: [----------] 3 tests from PmeTest (93927 ms total)
46:
46: [----------] 1 test from ReplicaExchangeTerminationTest
46: [ RUN ] ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts
46: [ OK ] ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (0 ms)
46: [----------] 1 test from ReplicaExchangeTerminationTest (0 ms total)
46:
46: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest
46: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 330891 of the 330891 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 330891 of the 330891 1-4 parameter combinations
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 27.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
46: Using 2 MPI threads
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads per tMPI thread
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Steepest Descents:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Steepest Descents did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = -4.7991020e+01
46: Maximum force = 1.8629866e+02 on atom 13
46: Norm of force = 8.7722033e+01
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (6282 ms)
46: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 330891 of the 330891 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 330891 of the 330891 1-4 parameter combinations
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 27.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
46: Using 2 MPI threads
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads per tMPI thread
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Polak-Ribiere Conjugate Gradients:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46: F-max = 3.02331e+02 on atom 3
46: F-Norm = 1.18024e+02
46:
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = -5.5862247e+01
46: Maximum force = 4.2727914e+02 on atom 13
46: Norm of force = 1.8453180e+02
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (7859 ms)
46: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 20503 of the 20503 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 1
46: Generated 17396 of the 20503 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Glycine'
46: Number of degrees of freedom in T-Coupling group System is 22.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
46: Using 2 MPI threads
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads per tMPI thread
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Steepest Descents:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Steepest Descents did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = 3.1937704e+02
46: Maximum force = 9.9988633e+03 on atom 9
46: Norm of force = 4.6166993e+03
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 turning H bonds into constraints...
46: This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (4230 ms)
46: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 20503 of the 20503 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 1
46: Generated 17396 of the 20503 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Glycine'
46:
46: NOTE 3 [file glycine_vacuo.top, line 12]:
46: For accurate cg with LINCS constraints, lincs-order should be 8 or more.
46:
46: Number of degrees of freedom in T-Coupling group System is 22.00
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
46: Using 2 MPI threads
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads per tMPI thread
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Polak-Ribiere Conjugate Gradients:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46: F-max = 2.41575e+04 on atom 10
46: F-Norm = 1.18451e+04
46:
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = 1.5174442e+02
46: Maximum force = 7.4208892e+03 on atom 9
46: Norm of force = 3.5693002e+03
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 turning H bonds into constraints...
46: This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (5822 ms)
46: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 2145 of the 2145 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2145 of the 2145 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
46:
46: NOTE 3 [file unknown]:
46: You are using constraints on all bonds, whereas the forcefield has been
46: parametrized only with constraints involving hydrogen atoms. We suggest
46: using constraints = h-bonds instead, this will also improve performance.
46:
46: Cleaning up constraints and constant bonded interactions with virtual sites
46: Removed 18 Angles with virtual sites, 21 left
46: Removed 10 Proper Dih.s with virtual sites, 44 left
46: Converted 15 Constraints with virtual sites to connections, 7 left
46: Number of degrees of freedom in T-Coupling group System is 23.00
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
46: Using 2 MPI threads
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads per tMPI thread
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Steepest Descents:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Steepest Descents did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = -1.5698419e+02
46: Maximum force = 4.5704996e+02 on atom 17
46: Norm of force = 1.8327748e+02
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 3.000
Last energy frame read 2 time 3.000 turning all bonds into constraints...
46: This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (4760 ms)
46: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 2145 of the 2145 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2145 of the 2145 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
46:
46: NOTE 3 [file unknown]:
46: You are using constraints on all bonds, whereas the forcefield has been
46: parametrized only with constraints involving hydrogen atoms. We suggest
46: using constraints = h-bonds instead, this will also improve performance.
46:
46:
46: NOTE 4 [file unknown]:
46: For accurate cg with LINCS constraints, lincs-order should be 8 or more.
46:
46: Cleaning up constraints and constant bonded interactions with virtual sites
46: Removed 18 Angles with virtual sites, 21 left
46: Removed 10 Proper Dih.s with virtual sites, 44 left
46: Converted 15 Constraints with virtual sites to connections, 7 left
46: Number of degrees of freedom in T-Coupling group System is 23.00
46:
46: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 5 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
46: Using 2 MPI threads
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads per tMPI thread
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Polak-Ribiere Conjugate Gradients:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46: F-max = 1.06801e+03 on atom 28
46: F-Norm = 4.26916e+02
46:
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = -1.6941193e+02
46: Maximum force = 2.1835349e+02 on atom 17
46: Norm of force = 7.9216550e+01
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 turning all bonds into constraints...
46: This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (7045 ms)
46: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (35998 ms total)
46:
46: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest
46: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 1 of the 1 non-bonded parameter combinations
46: Excluding 1 bonded neighbours molecule type 'Argon'
46: Number of degrees of freedom in T-Coupling group System is 33.00
46:
46: There were 2 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
46: Using 2 MPI threads
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads per tMPI thread
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Steepest Descents:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46:
46: writing lowest energy coordinates.
46:
46: Steepest Descents converged to Fmax < 10 in 1 steps
46: Potential Energy = -9.7425699e-01
46: Maximum force = 4.0132303e+00 on atom 3
46: Norm of force = 1.6383944e+00
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (1634 ms)
46: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 1 of the 1 non-bonded parameter combinations
46: Excluding 1 bonded neighbours molecule type 'Argon'
46: Number of degrees of freedom in T-Coupling group System is 33.00
46:
46: There were 2 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
46: Using 2 MPI threads
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads per tMPI thread
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Polak-Ribiere Conjugate Gradients:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46: F-max = 4.01323e+00 on atom 3
46: F-Norm = 1.63839e+00
46:
46:
46: writing lowest energy coordinates.
46:
46: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps
46: Potential Energy = -9.9064207e-01
46: Maximum force = 2.5781622e+00 on atom 3
46: Norm of force = 1.0525302e+00
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Last energy frame read 1 time 0.000 This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (2117 ms)
46: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46:
46: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
46: For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
46:
46: Generated 1 of the 1 non-bonded parameter combinations
46: Excluding 1 bonded neighbours molecule type 'Argon'
46: Number of degrees of freedom in T-Coupling group System is 33.00
46:
46: There were 2 notes
46:
46: There was 1 warning
46: This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (23 ms)
46: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 20503 of the 20503 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 1
46: Generated 17396 of the 20503 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Glycine'
46: Number of degrees of freedom in T-Coupling group System is 27.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
46: Using 2 MPI threads
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads per tMPI thread
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Steepest Descents:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Steepest Descents did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = 3.1939685e+02
46: Maximum force = 9.9704248e+03 on atom 9
46: Norm of force = 4.6227568e+03
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (3903 ms)
46: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 20503 of the 20503 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 1
46: Generated 17396 of the 20503 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Glycine'
46: Number of degrees of freedom in T-Coupling group System is 27.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
46: Using 2 MPI threads
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads per tMPI thread
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Polak-Ribiere Conjugate Gradients:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46: F-max = 2.41672e+04 on atom 10
46: F-Norm = 1.19357e+04
46:
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = 1.5625764e+02
46: Maximum force = 7.5018237e+03 on atom 9
46: Norm of force = 3.6139019e+03
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (5422 ms)
46: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46:
46: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
46: For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
46:
46: Generated 20503 of the 20503 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 1
46: Generated 17396 of the 20503 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Glycine'
46: Number of degrees of freedom in T-Coupling group System is 27.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46:
46: There was 1 warning
46: This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (1027 ms)
46: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (14127 ms total)
46:
46: [----------] Global test environment tear-down
46: [==========] 22 tests from 7 test cases ran. (152510 ms total)
46: [ PASSED ] 22 tests.
46:
46: YOU HAVE 4 DISABLED TESTS
46:
46/52 Test #46: MdrunMpiTests ....................... Passed 152.59 sec
test 47
Start 47: MdrunMpiCoordinationTestsOneRank
47: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrun-mpi-coordination-test "-ntmpi" "1" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunMpiCoordinationTestsOneRank.xml"
47: Test timeout computed to be: 480
47: [==========] Running 27 tests from 3 test cases.
47: [----------] Global test environment set-up.
47: [----------] 1 test from BasicPropagators/PeriodicActionsTest
47: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.190 0.190 99.9
47: (ns/day) (hour/ns)
47: Performance: 7.716 3.110
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.187 0.188 99.5
47: (ns/day) (hour/ns)
47: Performance: 7.797 3.078
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.193 0.194 99.5
47: (ns/day) (hour/ns)
47: Performance: 7.570 3.170
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.204 0.205 99.7
47: (ns/day) (hour/ns)
47: Performance: 7.180 3.343
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.200 0.201 99.8
47: (ns/day) (hour/ns)
47: Performance: 7.318 3.280
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.175 0.176 99.7
47: (ns/day) (hour/ns)
47: Performance: 8.351 2.874
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
47: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (1417 ms)
47: [----------] 1 test from BasicPropagators/PeriodicActionsTest (1417 ms total)
47:
47: [----------] 18 tests from PropagatorsWithCoupling/PeriodicActionsTest
47: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.148 0.148 99.8
47: (ns/day) (hour/ns)
47: Performance: 9.908 2.422
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.177 0.177 99.8
47: (ns/day) (hour/ns)
47: Performance: 8.284 2.897
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.161 0.162 99.7
47: (ns/day) (hour/ns)
47: Performance: 9.078 2.644
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.184 0.184 99.8
47: (ns/day) (hour/ns)
47: Performance: 7.968 3.012
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.175 0.175 99.7
47: (ns/day) (hour/ns)
47: Performance: 8.379 2.864
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.164 0.164 99.7
47: (ns/day) (hour/ns)
47: Performance: 8.956 2.680
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
47: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (1234 ms)
47: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.159 0.159 99.8
47: (ns/day) (hour/ns)
47: Performance: 9.216 2.604
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.133 0.133 99.7
47: (ns/day) (hour/ns)
47: Performance: 11.031 2.176
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.150 0.151 99.7
47: (ns/day) (hour/ns)
47: Performance: 9.745 2.463
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.206 0.206 99.7
47: (ns/day) (hour/ns)
47: Performance: 7.124 3.369
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.163 0.164 99.7
47: (ns/day) (hour/ns)
47: Performance: 8.972 2.675
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.152 0.153 99.6
47: (ns/day) (hour/ns)
47: Performance: 9.599 2.500
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
47: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (1189 ms)
47: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.169 0.170 99.8
47: (ns/day) (hour/ns)
47: Performance: 8.657 2.772
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.177 0.178 99.8
47: (ns/day) (hour/ns)
47: Performance: 8.272 2.901
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.184 0.184 99.7
47: (ns/day) (hour/ns)
47: Performance: 7.978 3.008
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.183 0.184 99.7
47: (ns/day) (hour/ns)
47: Performance: 7.987 3.005
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.219 0.219 99.7
47: (ns/day) (hour/ns)
47: Performance: 6.699 3.583
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.141 0.141 99.7
47: (ns/day) (hour/ns)
47: Performance: 10.395 2.309
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
47: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (1299 ms)
47: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.136 0.137 99.8
47: (ns/day) (hour/ns)
47: Performance: 10.759 2.231
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.177 0.178 99.8
47: (ns/day) (hour/ns)
47: Performance: 8.270 2.902
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.183 0.184 99.7
47: (ns/day) (hour/ns)
47: Performance: 7.993 3.002
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.194 0.195 99.8
47: (ns/day) (hour/ns)
47: Performance: 7.549 3.179
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.185 0.186 99.8
47: (ns/day) (hour/ns)
47: Performance: 7.906 3.035
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.163 0.164 99.7
47: (ns/day) (hour/ns)
47: Performance: 8.978 2.673
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
47: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (1266 ms)
47: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.137 0.137 99.8
47: (ns/day) (hour/ns)
47: Performance: 10.728 2.237
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.188 0.189 99.8
47: (ns/day) (hour/ns)
47: Performance: 7.789 3.081
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.172 0.172 99.7
47: (ns/day) (hour/ns)
47: Performance: 8.519 2.817
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.161 0.161 99.7
47: (ns/day) (hour/ns)
47: Performance: 9.110 2.634
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.174 0.174 99.7
47: (ns/day) (hour/ns)
47: Performance: 8.420 2.850
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.138 0.138 99.7
47: (ns/day) (hour/ns)
47: Performance: 10.635 2.257
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
47: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (1201 ms)
47: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.188 0.189 99.9
47: (ns/day) (hour/ns)
47: Performance: 7.789 3.081
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.187 0.188 99.8
47: (ns/day) (hour/ns)
47: Performance: 7.831 3.065
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.183 0.184 99.8
47: (ns/day) (hour/ns)
47: Performance: 8.002 2.999
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.205 0.206 99.8
47: (ns/day) (hour/ns)
47: Performance: 7.140 3.361
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.185 0.186 99.8
47: (ns/day) (hour/ns)
47: Performance: 7.912 3.033
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.185 0.185 99.8
47: (ns/day) (hour/ns)
47: Performance: 7.919 3.031
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
47: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (1364 ms)
47: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.136 0.137 99.8
47: (ns/day) (hour/ns)
47: Performance: 10.754 2.232
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.166 0.166 99.8
47: (ns/day) (hour/ns)
47: Performance: 8.825 2.720
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.160 0.161 99.6
47: (ns/day) (hour/ns)
47: Performance: 9.130 2.629
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.138 0.138 99.7
47: (ns/day) (hour/ns)
47: Performance: 10.631 2.257
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.162 0.163 99.7
47: (ns/day) (hour/ns)
47: Performance: 9.016 2.662
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.162 0.163 99.7
47: (ns/day) (hour/ns)
47: Performance: 9.021 2.660
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
47: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (1156 ms)
47: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
47:
47:
47: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: Using Berendsen pressure coupling invalidates the true ensemble for the
47: thermostat
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 3 notes
47:
47: There was 1 warning
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.132 0.132 99.8
47: (ns/day) (hour/ns)
47: Performance: 11.090 2.164
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
47:
47:
47: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: Using Berendsen pressure coupling invalidates the true ensemble for the
47: thermostat
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 3 notes
47:
47: There was 1 warning
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.176 0.177 99.8
47: (ns/day) (hour/ns)
47: Performance: 8.316 2.886
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
47:
47:
47: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: Using Berendsen pressure coupling invalidates the true ensemble for the
47: thermostat
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 3 notes
47:
47: There was 1 warning
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.160 0.161 99.7
47: (ns/day) (hour/ns)
47: Performance: 9.128 2.629
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
47:
47:
47: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: Using Berendsen pressure coupling invalidates the true ensemble for the
47: thermostat
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 3 notes
47:
47: There was 1 warning
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.160 0.161 99.7
47: (ns/day) (hour/ns)
47: Performance: 9.140 2.626
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
47:
47:
47: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: Using Berendsen pressure coupling invalidates the true ensemble for the
47: thermostat
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 3 notes
47:
47: There was 1 warning
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.195 0.195 99.8
47: (ns/day) (hour/ns)
47: Performance: 7.531 3.187
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
47:
47:
47: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: Using Berendsen pressure coupling invalidates the true ensemble for the
47: thermostat
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 3 notes
47:
47: There was 1 warning
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.240 0.240 99.8
47: (ns/day) (hour/ns)
47: Performance: 6.108 3.929
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
47: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (1299 ms)
47: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
47: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.147 0.147 99.8
47: (ns/day) (hour/ns)
47: Performance: 9.959 2.410
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
47: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.199 0.199 99.8
47: (ns/day) (hour/ns)
47: Performance: 7.370 3.257
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
47: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.239 0.239 99.8
47: (ns/day) (hour/ns)
47: Performance: 6.145 3.906
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
47: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.249 0.250 99.7
47: (ns/day) (hour/ns)
47: Performance: 5.872 4.087
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
47: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.185 0.185 99.7
47: (ns/day) (hour/ns)
47: Performance: 7.926 3.028
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
47: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.157 0.158 99.7
47: (ns/day) (hour/ns)
47: Performance: 9.318 2.576
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
47: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (1433 ms)
47: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.151 0.151 99.8
47: (ns/day) (hour/ns)
47: Performance: 9.741 2.464
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.158 0.158 99.8
47: (ns/day) (hour/ns)
47: Performance: 9.289 2.584
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.164 0.165 99.3
47: (ns/day) (hour/ns)
47: Performance: 8.918 2.691
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.186 0.187 99.5
47: (ns/day) (hour/ns)
47: Performance: 7.873 3.048
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.141 0.142 99.4
47: (ns/day) (hour/ns)
47: Performance: 10.326 2.324
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.155 0.156 99.7
47: (ns/day) (hour/ns)
47: Performance: 9.445 2.541
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
47: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (1166 ms)
47: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.173 0.174 99.9
47: (ns/day) (hour/ns)
47: Performance: 8.455 2.838
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.135 0.136 99.8
47: (ns/day) (hour/ns)
47: Performance: 10.813 2.220
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.243 0.243 99.8
47: (ns/day) (hour/ns)
47: Performance: 6.043 3.972
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.176 0.177 99.7
47: (ns/day) (hour/ns)
47: Performance: 8.314 2.887
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.244 0.244 99.8
47: (ns/day) (hour/ns)
47: Performance: 6.011 3.993
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.200 0.200 99.7
47: (ns/day) (hour/ns)
47: Performance: 7.334 3.272
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
47: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (1378 ms)
47: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.251 0.251 99.9
47: (ns/day) (hour/ns)
47: Performance: 5.845 4.106
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.158 0.158 99.8
47: (ns/day) (hour/ns)
47: Performance: 9.284 2.585
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.287 0.287 99.8
47: (ns/day) (hour/ns)
47: Performance: 5.113 4.694
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.252 0.252 99.8
47: (ns/day) (hour/ns)
47: Performance: 5.823 4.122
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.146 0.146 99.7
47: (ns/day) (hour/ns)
47: Performance: 10.032 2.392
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.144 0.145 99.7
47: (ns/day) (hour/ns)
47: Performance: 10.160 2.362
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
47: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (1445 ms)
47: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.274 0.274 99.9
47: (ns/day) (hour/ns)
47: Performance: 5.361 4.476
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.147 0.148 99.9
47: (ns/day) (hour/ns)
47: Performance: 9.949 2.412
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.269 0.269 99.9
47: (ns/day) (hour/ns)
47: Performance: 5.458 4.397
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.183 0.183 99.9
47: (ns/day) (hour/ns)
47: Performance: 8.007 2.997
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 1.005 1.005 100.0
47: (ns/day) (hour/ns)
47: Performance: 1.462 16.417
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.187 0.187 99.9
47: (ns/day) (hour/ns)
47: Performance: 7.854 3.056
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
47: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (2278 ms)
47: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.261 0.262 99.9
47: (ns/day) (hour/ns)
47: Performance: 5.614 4.275
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.191 0.192 99.8
47: (ns/day) (hour/ns)
47: Performance: 7.656 3.135
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.298 0.299 99.8
47: (ns/day) (hour/ns)
47: Performance: 4.917 4.881
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.153 0.154 99.6
47: (ns/day) (hour/ns)
47: Performance: 9.537 2.516
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.266 0.267 99.8
47: (ns/day) (hour/ns)
47: Performance: 5.506 4.359
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.166 0.167 99.6
47: (ns/day) (hour/ns)
47: Performance: 8.800 2.727
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file
47: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (1544 ms)
47: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.262 0.263 99.9
47: (ns/day) (hour/ns)
47: Performance: 5.594 4.291
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.169 0.170 99.9
47: (ns/day) (hour/ns)
47: Performance: 8.662 2.771
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.265 0.266 99.9
47: (ns/day) (hour/ns)
47: Performance: 5.529 4.341
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.176 0.177 99.9
47: (ns/day) (hour/ns)
47: Performance: 8.317 2.886
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.256 0.256 99.9
47: (ns/day) (hour/ns)
47: Performance: 5.741 4.180
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.156 0.156 99.9
47: (ns/day) (hour/ns)
47: Performance: 9.422 2.547
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file
47: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (1489 ms)
47: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.251 0.251 99.9
47: (ns/day) (hour/ns)
47: Performance: 5.854 4.100
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.147 0.147 99.7
47: (ns/day) (hour/ns)
47: Performance: 9.984 2.404
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.254 0.254 99.8
47: (ns/day) (hour/ns)
47: Performance: 5.779 4.153
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.309 0.309 99.8
47: (ns/day) (hour/ns)
47: Performance: 4.750 5.053
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.176 0.177 99.7
47: (ns/day) (hour/ns)
47: Performance: 8.299 2.892
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.255 0.255 99.8
47: (ns/day) (hour/ns)
47: Performance: 5.753 4.172
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file
47: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (1600 ms)
47: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.173 0.173 99.9
47: (ns/day) (hour/ns)
47: Performance: 8.474 2.832
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.258 0.258 99.9
47: (ns/day) (hour/ns)
47: Performance: 5.688 4.219
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.143 0.144 99.4
47: (ns/day) (hour/ns)
47: Performance: 10.192 2.355
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.231 0.232 99.6
47: (ns/day) (hour/ns)
47: Performance: 6.322 3.796
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.152 0.153 99.4
47: (ns/day) (hour/ns)
47: Performance: 9.577 2.506
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.243 0.244 99.6
47: (ns/day) (hour/ns)
47: Performance: 6.019 3.987
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file
47: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (1413 ms)
47: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.149 0.149 99.8
47: (ns/day) (hour/ns)
47: Performance: 9.855 2.435
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.246 0.247 99.7
47: (ns/day) (hour/ns)
47: Performance: 5.943 4.038
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.152 0.153 99.4
47: (ns/day) (hour/ns)
47: Performance: 9.586 2.504
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.241 0.242 99.6
47: (ns/day) (hour/ns)
47: Performance: 6.072 3.952
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.142 0.143 99.3
47: (ns/day) (hour/ns)
47: Performance: 10.249 2.342
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.186 0.187 99.5
47: (ns/day) (hour/ns)
47: Performance: 7.838 3.062
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file
47: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (1333 ms)
47: [----------] 18 tests from PropagatorsWithCoupling/PeriodicActionsTest (25091 ms total)
47:
47: [----------] 8 tests from PropagatorsWithConstraints/PeriodicActionsTest
47: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: NVE simulation: will use the initial temperature of 398.997 K for
47: determining the Verlet buffer size
47:
47:
47: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 4 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
47: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.245 0.245 99.9
47: (ns/day) (hour/ns)
47: Performance: 5.992 4.006
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: NVE simulation: will use the initial temperature of 398.997 K for
47: determining the Verlet buffer size
47:
47:
47: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 4 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
47: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.251 0.252 99.9
47: (ns/day) (hour/ns)
47: Performance: 5.833 4.115
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: NVE simulation: will use the initial temperature of 398.997 K for
47: determining the Verlet buffer size
47:
47:
47: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 4 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
47: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.254 0.254 99.8
47: (ns/day) (hour/ns)
47: Performance: 5.780 4.153
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: NVE simulation: will use the initial temperature of 398.997 K for
47: determining the Verlet buffer size
47:
47:
47: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 4 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
47: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.260 0.261 99.6
47: (ns/day) (hour/ns)
47: Performance: 5.634 4.260
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: NVE simulation: will use the initial temperature of 398.997 K for
47: determining the Verlet buffer size
47:
47:
47: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 4 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
47: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.267 0.268 99.6
47: (ns/day) (hour/ns)
47: Performance: 5.477 4.382
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: NVE simulation: will use the initial temperature of 398.997 K for
47: determining the Verlet buffer size
47:
47:
47: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 4 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
47: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.245 0.245 99.8
47: (ns/day) (hour/ns)
47: Performance: 5.990 4.007
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
47: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (21022 ms)
47: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: NVE simulation: will use the initial temperature of 398.997 K for
47: determining the Verlet buffer size
47:
47:
47: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 4 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
47: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.286 0.286 99.9
47: (ns/day) (hour/ns)
47: Performance: 5.134 4.675
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: NVE simulation: will use the initial temperature of 398.997 K for
47: determining the Verlet buffer size
47:
47:
47: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 4 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
47: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.224 0.224 99.8
47: (ns/day) (hour/ns)
47: Performance: 6.547 3.666
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: NVE simulation: will use the initial temperature of 398.997 K for
47: determining the Verlet buffer size
47:
47:
47: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 4 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
47: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.206 0.207 99.7
47: (ns/day) (hour/ns)
47: Performance: 7.101 3.380
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: NVE simulation: will use the initial temperature of 398.997 K for
47: determining the Verlet buffer size
47:
47:
47: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 4 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
47: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.263 0.264 99.8
47: (ns/day) (hour/ns)
47: Performance: 5.574 4.306
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: NVE simulation: will use the initial temperature of 398.997 K for
47: determining the Verlet buffer size
47:
47:
47: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 4 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
47: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.220 0.221 99.7
47: (ns/day) (hour/ns)
47: Performance: 6.647 3.611
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: NVE simulation: will use the initial temperature of 398.997 K for
47: determining the Verlet buffer size
47:
47:
47: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 4 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
47: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.213 0.213 99.7
47: (ns/day) (hour/ns)
47: Performance: 6.881 3.488
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
47: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (21032 ms)
47: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.241 0.241 99.9
47: (ns/day) (hour/ns)
47: Performance: 6.087 3.943
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.148 0.148 99.8
47: (ns/day) (hour/ns)
47: Performance: 9.893 2.426
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.237 0.237 99.8
47: (ns/day) (hour/ns)
47: Performance: 6.195 3.874
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.242 0.242 99.8
47: (ns/day) (hour/ns)
47: Performance: 6.068 3.955
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.207 0.207 99.7
47: (ns/day) (hour/ns)
47: Performance: 7.079 3.390
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.252 0.253 99.8
47: (ns/day) (hour/ns)
47: Performance: 5.817 4.126
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
47: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (20492 ms)
47: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.257 0.257 99.9
47: (ns/day) (hour/ns)
47: Performance: 5.720 4.196
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.285 0.286 99.9
47: (ns/day) (hour/ns)
47: Performance: 5.140 4.669
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.244 0.244 99.8
47: (ns/day) (hour/ns)
47: Performance: 6.008 3.995
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.256 0.257 99.8
47: (ns/day) (hour/ns)
47: Performance: 5.724 4.193
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.124 0.125 99.6
47: (ns/day) (hour/ns)
47: Performance: 11.764 2.040
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.218 0.218 99.8
47: (ns/day) (hour/ns)
47: Performance: 6.734 3.564
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
47: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (20477 ms)
47: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.228 0.228 99.9
47: (ns/day) (hour/ns)
47: Performance: 6.448 3.722
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.234 0.234 99.8
47: (ns/day) (hour/ns)
47: Performance: 6.268 3.829
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.203 0.204 99.7
47: (ns/day) (hour/ns)
47: Performance: 7.213 3.327
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.449 0.449 99.9
47: (ns/day) (hour/ns)
47: Performance: 3.271 7.338
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.251 0.252 99.8
47: (ns/day) (hour/ns)
47: Performance: 5.830 4.116
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.240 0.240 99.8
47: (ns/day) (hour/ns)
47: Performance: 6.115 3.925
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
47: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (20669 ms)
47: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.284 0.284 99.9
47: (ns/day) (hour/ns)
47: Performance: 5.170 4.642
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.229 0.230 99.8
47: (ns/day) (hour/ns)
47: Performance: 6.395 3.753
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.241 0.242 99.8
47: (ns/day) (hour/ns)
47: Performance: 6.074 3.951
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.144 0.144 99.7
47: (ns/day) (hour/ns)
47: Performance: 10.193 2.355
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.225 0.226 99.8
47: (ns/day) (hour/ns)
47: Performance: 6.507 3.689
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.239 0.239 99.8
47: (ns/day) (hour/ns)
47: Performance: 6.141 3.908
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
47: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (20445 ms)
47: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: NVE simulation: will use the initial temperature of 398.997 K for
47: determining the Verlet buffer size
47:
47:
47: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 4 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
47: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.288 0.288 99.9
47: (ns/day) (hour/ns)
47: Performance: 5.094 4.711
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: NVE simulation: will use the initial temperature of 398.997 K for
47: determining the Verlet buffer size
47:
47:
47: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 4 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
47: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.236 0.236 99.9
47: (ns/day) (hour/ns)
47: Performance: 6.212 3.864
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: NVE simulation: will use the initial temperature of 398.997 K for
47: determining the Verlet buffer size
47:
47:
47: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 4 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
47: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.228 0.228 99.9
47: (ns/day) (hour/ns)
47: Performance: 6.444 3.724
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: NVE simulation: will use the initial temperature of 398.997 K for
47: determining the Verlet buffer size
47:
47:
47: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 4 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
47: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.222 0.222 99.9
47: (ns/day) (hour/ns)
47: Performance: 6.613 3.629
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: NVE simulation: will use the initial temperature of 398.997 K for
47: determining the Verlet buffer size
47:
47:
47: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 4 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
47: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.206 0.207 99.9
47: (ns/day) (hour/ns)
47: Performance: 7.109 3.376
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: NVE simulation: will use the initial temperature of 398.997 K for
47: determining the Verlet buffer size
47:
47:
47: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 4 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
47: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.181 0.181 99.9
47: (ns/day) (hour/ns)
47: Performance: 8.112 2.959
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
47: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (20434 ms)
47: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.239 0.240 99.9
47: (ns/day) (hour/ns)
47: Performance: 6.130 3.915
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.224 0.224 99.9
47: (ns/day) (hour/ns)
47: Performance: 6.560 3.658
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.237 0.237 99.9
47: (ns/day) (hour/ns)
47: Performance: 6.204 3.868
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.282 0.282 99.9
47: (ns/day) (hour/ns)
47: Performance: 5.202 4.614
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.168 0.168 99.9
47: (ns/day) (hour/ns)
47: Performance: 8.732 2.749
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.160 0.160 99.9
47: (ns/day) (hour/ns)
47: Performance: 9.175 2.616
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
47: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (20390 ms)
47: [----------] 8 tests from PropagatorsWithConstraints/PeriodicActionsTest (164961 ms total)
47:
47: [----------] Global test environment tear-down
47: [==========] 27 tests from 3 test cases ran. (191470 ms total)
47: [ PASSED ] 27 tests.
47/52 Test #47: MdrunMpiCoordinationTestsOneRank .... Passed 191.55 sec
test 48
Start 48: MdrunMpiCoordinationTestsTwoRanks
48: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrun-mpi-coordination-test "-ntmpi" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunMpiCoordinationTestsTwoRanks.xml"
48: Test timeout computed to be: 480
48: [==========] Running 27 tests from 3 test cases.
48: [----------] Global test environment set-up.
48: [----------] 1 test from BasicPropagators/PeriodicActionsTest
48: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.356 0.178 199.7
48: (ns/day) (hour/ns)
48: Performance: 8.237 2.914
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.332 0.166 199.3
48: (ns/day) (hour/ns)
48: Performance: 8.826 2.719
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.305 0.153 199.2
48: (ns/day) (hour/ns)
48: Performance: 9.601 2.500
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.322 0.162 198.5
48: (ns/day) (hour/ns)
48: Performance: 9.066 2.647
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.304 0.153 198.6
48: (ns/day) (hour/ns)
48: Performance: 9.581 2.505
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.334 0.169 197.8
48: (ns/day) (hour/ns)
48: Performance: 8.698 2.759
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
48: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (1254 ms)
48: [----------] 1 test from BasicPropagators/PeriodicActionsTest (1254 ms total)
48:
48: [----------] 18 tests from PropagatorsWithCoupling/PeriodicActionsTest
48: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.351 0.176 199.6
48: (ns/day) (hour/ns)
48: Performance: 8.347 2.875
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.314 0.158 198.7
48: (ns/day) (hour/ns)
48: Performance: 9.288 2.584
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.330 0.166 198.6
48: (ns/day) (hour/ns)
48: Performance: 8.845 2.714
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.308 0.155 198.7
48: (ns/day) (hour/ns)
48: Performance: 9.467 2.535
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.312 0.157 198.6
48: (ns/day) (hour/ns)
48: Performance: 9.339 2.570
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.357 0.179 198.9
48: (ns/day) (hour/ns)
48: Performance: 8.186 2.932
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
48: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (1302 ms)
48: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.374 0.188 199.6
48: (ns/day) (hour/ns)
48: Performance: 7.830 3.065
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.385 0.194 198.9
48: (ns/day) (hour/ns)
48: Performance: 7.587 3.163
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.398 0.200 198.8
48: (ns/day) (hour/ns)
48: Performance: 7.333 3.273
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.349 0.176 198.5
48: (ns/day) (hour/ns)
48: Performance: 8.365 2.869
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.356 0.179 198.6
48: (ns/day) (hour/ns)
48: Performance: 8.199 2.927
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.288 0.145 198.3
48: (ns/day) (hour/ns)
48: Performance: 10.118 2.372
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
48: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (1411 ms)
48: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.351 0.176 199.6
48: (ns/day) (hour/ns)
48: Performance: 8.346 2.876
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.296 0.149 198.7
48: (ns/day) (hour/ns)
48: Performance: 9.873 2.431
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.351 0.177 198.6
48: (ns/day) (hour/ns)
48: Performance: 8.307 2.889
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.306 0.154 198.4
48: (ns/day) (hour/ns)
48: Performance: 9.525 2.520
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.310 0.156 198.3
48: (ns/day) (hour/ns)
48: Performance: 9.394 2.555
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.332 0.168 198.4
48: (ns/day) (hour/ns)
48: Performance: 8.765 2.738
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
48: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (1310 ms)
48: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.352 0.176 199.6
48: (ns/day) (hour/ns)
48: Performance: 8.338 2.878
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.321 0.161 198.7
48: (ns/day) (hour/ns)
48: Performance: 9.103 2.636
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.330 0.166 198.6
48: (ns/day) (hour/ns)
48: Performance: 8.842 2.714
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.281 0.141 199.1
48: (ns/day) (hour/ns)
48: Performance: 10.392 2.309
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.306 0.153 199.2
48: (ns/day) (hour/ns)
48: Performance: 9.572 2.507
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.372 0.187 199.3
48: (ns/day) (hour/ns)
48: Performance: 7.874 3.048
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
48: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (1270 ms)
48: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.324 0.162 199.6
48: (ns/day) (hour/ns)
48: Performance: 9.055 2.650
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.419 0.210 199.6
48: (ns/day) (hour/ns)
48: Performance: 6.996 3.430
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.392 0.197 199.2
48: (ns/day) (hour/ns)
48: Performance: 7.471 3.212
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.494 0.248 199.3
48: (ns/day) (hour/ns)
48: Performance: 5.923 4.052
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.302 0.152 199.1
48: (ns/day) (hour/ns)
48: Performance: 9.674 2.481
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.453 0.227 199.4
48: (ns/day) (hour/ns)
48: Performance: 6.466 3.712
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
48: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (1422 ms)
48: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.324 0.162 199.5
48: (ns/day) (hour/ns)
48: Performance: 9.059 2.649
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.464 0.232 199.6
48: (ns/day) (hour/ns)
48: Performance: 6.323 3.796
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.369 0.185 199.4
48: (ns/day) (hour/ns)
48: Performance: 7.946 3.020
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.473 0.237 199.5
48: (ns/day) (hour/ns)
48: Performance: 6.198 3.872
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.323 0.162 199.4
48: (ns/day) (hour/ns)
48: Performance: 9.077 2.644
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.461 0.231 199.5
48: (ns/day) (hour/ns)
48: Performance: 6.361 3.773
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
48: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (1433 ms)
48: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.338 0.169 199.6
48: (ns/day) (hour/ns)
48: Performance: 8.671 2.768
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.506 0.254 199.6
48: (ns/day) (hour/ns)
48: Performance: 5.790 4.145
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.295 0.148 199.3
48: (ns/day) (hour/ns)
48: Performance: 9.934 2.416
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.458 0.230 199.4
48: (ns/day) (hour/ns)
48: Performance: 6.392 3.754
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.371 0.186 199.4
48: (ns/day) (hour/ns)
48: Performance: 7.884 3.044
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.550 0.276 199.5
48: (ns/day) (hour/ns)
48: Performance: 5.331 4.502
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
48: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (1489 ms)
48: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
48:
48:
48: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: Using Berendsen pressure coupling invalidates the true ensemble for the
48: thermostat
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 3 notes
48:
48: There was 1 warning
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.345 0.173 199.6
48: (ns/day) (hour/ns)
48: Performance: 8.488 2.828
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
48:
48:
48: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: Using Berendsen pressure coupling invalidates the true ensemble for the
48: thermostat
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 3 notes
48:
48: There was 1 warning
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.552 0.277 199.6
48: (ns/day) (hour/ns)
48: Performance: 5.312 4.518
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
48:
48:
48: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: Using Berendsen pressure coupling invalidates the true ensemble for the
48: thermostat
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 3 notes
48:
48: There was 1 warning
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.301 0.151 199.0
48: (ns/day) (hour/ns)
48: Performance: 9.705 2.473
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
48:
48:
48: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: Using Berendsen pressure coupling invalidates the true ensemble for the
48: thermostat
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 3 notes
48:
48: There was 1 warning
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.478 0.240 199.4
48: (ns/day) (hour/ns)
48: Performance: 6.124 3.919
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
48:
48:
48: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: Using Berendsen pressure coupling invalidates the true ensemble for the
48: thermostat
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 3 notes
48:
48: There was 1 warning
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.305 0.153 199.1
48: (ns/day) (hour/ns)
48: Performance: 9.598 2.500
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
48:
48:
48: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: Using Berendsen pressure coupling invalidates the true ensemble for the
48: thermostat
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 3 notes
48:
48: There was 1 warning
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.482 0.242 199.3
48: (ns/day) (hour/ns)
48: Performance: 6.070 3.954
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
48: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (1456 ms)
48: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
48: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.301 0.151 199.5
48: (ns/day) (hour/ns)
48: Performance: 9.747 2.462
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
48: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.499 0.250 199.6
48: (ns/day) (hour/ns)
48: Performance: 5.876 4.085
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
48: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.339 0.170 199.2
48: (ns/day) (hour/ns)
48: Performance: 8.626 2.782
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
48: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.501 0.251 199.4
48: (ns/day) (hour/ns)
48: Performance: 5.848 4.104
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
48: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.303 0.152 199.1
48: (ns/day) (hour/ns)
48: Performance: 9.643 2.489
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
48: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.504 0.252 199.4
48: (ns/day) (hour/ns)
48: Performance: 5.817 4.126
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
48: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (1456 ms)
48: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.300 0.150 199.6
48: (ns/day) (hour/ns)
48: Performance: 9.776 2.455
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.485 0.243 199.6
48: (ns/day) (hour/ns)
48: Performance: 6.046 3.970
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.363 0.182 199.4
48: (ns/day) (hour/ns)
48: Performance: 8.079 2.971
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.591 0.296 199.6
48: (ns/day) (hour/ns)
48: Performance: 4.962 4.837
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.505 0.253 199.6
48: (ns/day) (hour/ns)
48: Performance: 5.808 4.132
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.392 0.197 199.4
48: (ns/day) (hour/ns)
48: Performance: 7.462 3.216
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
48: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (1544 ms)
48: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.406 0.203 199.7
48: (ns/day) (hour/ns)
48: Performance: 7.226 3.321
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.326 0.164 199.4
48: (ns/day) (hour/ns)
48: Performance: 8.975 2.674
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.478 0.240 199.4
48: (ns/day) (hour/ns)
48: Performance: 6.125 3.918
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.366 0.184 199.2
48: (ns/day) (hour/ns)
48: Performance: 7.985 3.006
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.519 0.261 199.3
48: (ns/day) (hour/ns)
48: Performance: 5.638 4.257
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.317 0.160 198.9
48: (ns/day) (hour/ns)
48: Performance: 9.207 2.607
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
48: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (1446 ms)
48: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.496 0.248 199.7
48: (ns/day) (hour/ns)
48: Performance: 5.912 4.059
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.306 0.153 199.4
48: (ns/day) (hour/ns)
48: Performance: 9.569 2.508
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.477 0.239 199.3
48: (ns/day) (hour/ns)
48: Performance: 6.135 3.912
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.339 0.170 199.0
48: (ns/day) (hour/ns)
48: Performance: 8.619 2.784
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.503 0.252 199.4
48: (ns/day) (hour/ns)
48: Performance: 5.818 4.125
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.260 0.131 198.9
48: (ns/day) (hour/ns)
48: Performance: 11.250 2.133
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
48: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (1421 ms)
48: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.538 0.270 199.5
48: (ns/day) (hour/ns)
48: Performance: 5.447 4.406
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.394 0.198 199.0
48: (ns/day) (hour/ns)
48: Performance: 7.420 3.235
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.452 0.227 199.3
48: (ns/day) (hour/ns)
48: Performance: 6.472 3.709
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.387 0.195 198.9
48: (ns/day) (hour/ns)
48: Performance: 7.550 3.179
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.432 0.217 198.9
48: (ns/day) (hour/ns)
48: Performance: 6.769 3.546
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.282 0.142 198.7
48: (ns/day) (hour/ns)
48: Performance: 10.357 2.317
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
48: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (1478 ms)
48: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.494 0.248 199.7
48: (ns/day) (hour/ns)
48: Performance: 5.932 4.046
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.307 0.154 199.4
48: (ns/day) (hour/ns)
48: Performance: 9.529 2.519
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.474 0.238 199.4
48: (ns/day) (hour/ns)
48: Performance: 6.182 3.882
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.294 0.148 199.1
48: (ns/day) (hour/ns)
48: Performance: 9.953 2.411
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.480 0.240 199.5
48: (ns/day) (hour/ns)
48: Performance: 6.108 3.930
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.321 0.161 199.2
48: (ns/day) (hour/ns)
48: Performance: 9.103 2.636
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file
48: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (1423 ms)
48: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.476 0.239 199.4
48: (ns/day) (hour/ns)
48: Performance: 6.152 3.901
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.456 0.229 199.1
48: (ns/day) (hour/ns)
48: Performance: 6.415 3.741
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.297 0.150 198.7
48: (ns/day) (hour/ns)
48: Performance: 9.819 2.444
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.478 0.240 199.3
48: (ns/day) (hour/ns)
48: Performance: 6.123 3.920
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.482 0.242 199.3
48: (ns/day) (hour/ns)
48: Performance: 6.072 3.953
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.481 0.242 199.3
48: (ns/day) (hour/ns)
48: Performance: 6.080 3.948
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file
48: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (1566 ms)
48: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.410 0.205 199.6
48: (ns/day) (hour/ns)
48: Performance: 7.158 3.353
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.373 0.187 199.5
48: (ns/day) (hour/ns)
48: Performance: 7.846 3.059
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.278 0.140 199.0
48: (ns/day) (hour/ns)
48: Performance: 10.521 2.281
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 1.977 0.990 199.8
48: (ns/day) (hour/ns)
48: Performance: 1.484 16.168
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.381 0.191 199.2
48: (ns/day) (hour/ns)
48: Performance: 7.682 3.124
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.481 0.241 199.4
48: (ns/day) (hour/ns)
48: Performance: 6.095 3.938
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file
48: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (2178 ms)
48: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.515 0.258 199.7
48: (ns/day) (hour/ns)
48: Performance: 5.696 4.214
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.333 0.167 199.5
48: (ns/day) (hour/ns)
48: Performance: 8.791 2.730
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.524 0.263 199.6
48: (ns/day) (hour/ns)
48: Performance: 5.595 4.289
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.546 0.273 199.6
48: (ns/day) (hour/ns)
48: Performance: 5.373 4.467
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.504 0.253 199.6
48: (ns/day) (hour/ns)
48: Performance: 5.815 4.127
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.454 0.228 199.4
48: (ns/day) (hour/ns)
48: Performance: 6.452 3.720
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file
48: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (1667 ms)
48: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.276 0.138 199.5
48: (ns/day) (hour/ns)
48: Performance: 10.614 2.261
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.435 0.218 199.6
48: (ns/day) (hour/ns)
48: Performance: 6.739 3.562
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.521 0.261 199.5
48: (ns/day) (hour/ns)
48: Performance: 5.623 4.268
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.361 0.181 199.2
48: (ns/day) (hour/ns)
48: Performance: 8.096 2.964
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.524 0.262 199.5
48: (ns/day) (hour/ns)
48: Performance: 5.596 4.289
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.525 0.263 199.4
48: (ns/day) (hour/ns)
48: Performance: 5.580 4.301
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file
48: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (1555 ms)
48: [----------] 18 tests from PropagatorsWithCoupling/PeriodicActionsTest (26830 ms total)
48:
48: [----------] 8 tests from PropagatorsWithConstraints/PeriodicActionsTest
48: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: NVE simulation: will use the initial temperature of 398.997 K for
48: determining the Verlet buffer size
48:
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
48: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.542 0.271 199.7
48: (ns/day) (hour/ns)
48: Performance: 5.414 4.433
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: NVE simulation: will use the initial temperature of 398.997 K for
48: determining the Verlet buffer size
48:
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
48: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.447 0.224 199.6
48: (ns/day) (hour/ns)
48: Performance: 6.555 3.661
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: NVE simulation: will use the initial temperature of 398.997 K for
48: determining the Verlet buffer size
48:
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
48: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.531 0.266 199.5
48: (ns/day) (hour/ns)
48: Performance: 5.518 4.349
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: NVE simulation: will use the initial temperature of 398.997 K for
48: determining the Verlet buffer size
48:
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
48: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.467 0.234 199.4
48: (ns/day) (hour/ns)
48: Performance: 6.277 3.823
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: NVE simulation: will use the initial temperature of 398.997 K for
48: determining the Verlet buffer size
48:
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
48: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.479 0.240 199.4
48: (ns/day) (hour/ns)
48: Performance: 6.116 3.924
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: NVE simulation: will use the initial temperature of 398.997 K for
48: determining the Verlet buffer size
48:
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
48: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.485 0.243 199.4
48: (ns/day) (hour/ns)
48: Performance: 6.038 3.975
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
48: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (20924 ms)
48: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: NVE simulation: will use the initial temperature of 398.997 K for
48: determining the Verlet buffer size
48:
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
48: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.427 0.214 199.6
48: (ns/day) (hour/ns)
48: Performance: 6.860 3.499
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: NVE simulation: will use the initial temperature of 398.997 K for
48: determining the Verlet buffer size
48:
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
48: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.491 0.246 199.5
48: (ns/day) (hour/ns)
48: Performance: 5.966 4.023
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: NVE simulation: will use the initial temperature of 398.997 K for
48: determining the Verlet buffer size
48:
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
48: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.414 0.208 199.3
48: (ns/day) (hour/ns)
48: Performance: 7.067 3.396
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: NVE simulation: will use the initial temperature of 398.997 K for
48: determining the Verlet buffer size
48:
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
48: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.468 0.235 199.4
48: (ns/day) (hour/ns)
48: Performance: 6.255 3.837
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: NVE simulation: will use the initial temperature of 398.997 K for
48: determining the Verlet buffer size
48:
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
48: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.495 0.249 198.9
48: (ns/day) (hour/ns)
48: Performance: 5.900 4.068
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: NVE simulation: will use the initial temperature of 398.997 K for
48: determining the Verlet buffer size
48:
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
48: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.535 0.269 199.0
48: (ns/day) (hour/ns)
48: Performance: 5.460 4.396
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
48: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (20719 ms)
48: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.491 0.246 199.7
48: (ns/day) (hour/ns)
48: Performance: 5.975 4.017
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.502 0.252 199.1
48: (ns/day) (hour/ns)
48: Performance: 5.821 4.123
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.496 0.249 199.0
48: (ns/day) (hour/ns)
48: Performance: 5.897 4.070
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.508 0.255 199.0
48: (ns/day) (hour/ns)
48: Performance: 5.756 4.170
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.446 0.224 198.9
48: (ns/day) (hour/ns)
48: Performance: 6.548 3.665
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.485 0.243 199.5
48: (ns/day) (hour/ns)
48: Performance: 6.044 3.971
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
48: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (20803 ms)
48: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.528 0.264 199.6
48: (ns/day) (hour/ns)
48: Performance: 5.556 4.319
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.497 0.249 199.6
48: (ns/day) (hour/ns)
48: Performance: 5.902 4.066
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.522 0.262 199.5
48: (ns/day) (hour/ns)
48: Performance: 5.617 4.273
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.529 0.266 198.7
48: (ns/day) (hour/ns)
48: Performance: 5.513 4.354
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.540 0.271 199.5
48: (ns/day) (hour/ns)
48: Performance: 5.426 4.423
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.496 0.249 199.5
48: (ns/day) (hour/ns)
48: Performance: 5.905 4.064
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
48: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (20957 ms)
48: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.487 0.244 199.7
48: (ns/day) (hour/ns)
48: Performance: 6.018 3.988
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.446 0.224 199.4
48: (ns/day) (hour/ns)
48: Performance: 6.569 3.654
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.498 0.250 199.4
48: (ns/day) (hour/ns)
48: Performance: 5.882 4.080
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.525 0.263 199.5
48: (ns/day) (hour/ns)
48: Performance: 5.577 4.303
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.536 0.269 199.4
48: (ns/day) (hour/ns)
48: Performance: 5.468 4.389
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.530 0.266 199.4
48: (ns/day) (hour/ns)
48: Performance: 5.527 4.342
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
48: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (20945 ms)
48: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.531 0.266 199.7
48: (ns/day) (hour/ns)
48: Performance: 5.523 4.345
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.499 0.250 199.5
48: (ns/day) (hour/ns)
48: Performance: 5.868 4.090
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.484 0.243 199.3
48: (ns/day) (hour/ns)
48: Performance: 6.044 3.971
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.514 0.258 199.3
48: (ns/day) (hour/ns)
48: Performance: 5.691 4.217
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.396 0.199 199.0
48: (ns/day) (hour/ns)
48: Performance: 7.377 3.254
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.314 0.158 198.8
48: (ns/day) (hour/ns)
48: Performance: 9.303 2.580
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
48: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (21013 ms)
48: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: NVE simulation: will use the initial temperature of 398.997 K for
48: determining the Verlet buffer size
48:
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
48: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.304 0.153 198.1
48: (ns/day) (hour/ns)
48: Performance: 9.582 2.505
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: NVE simulation: will use the initial temperature of 398.997 K for
48: determining the Verlet buffer size
48:
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
48: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.336 0.170 198.1
48: (ns/day) (hour/ns)
48: Performance: 8.652 2.774
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: NVE simulation: will use the initial temperature of 398.997 K for
48: determining the Verlet buffer size
48:
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
48: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.377 0.190 198.7
48: (ns/day) (hour/ns)
48: Performance: 7.745 3.099
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: NVE simulation: will use the initial temperature of 398.997 K for
48: determining the Verlet buffer size
48:
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
48: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.357 0.180 198.1
48: (ns/day) (hour/ns)
48: Performance: 8.160 2.941
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: NVE simulation: will use the initial temperature of 398.997 K for
48: determining the Verlet buffer size
48:
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
48: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.328 0.165 198.6
48: (ns/day) (hour/ns)
48: Performance: 8.899 2.697
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: NVE simulation: will use the initial temperature of 398.997 K for
48: determining the Verlet buffer size
48:
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
48: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.364 0.183 198.7
48: (ns/day) (hour/ns)
48: Performance: 8.024 2.991
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
48: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (21190 ms)
48: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.383 0.192 199.2
48: (ns/day) (hour/ns)
48: Performance: 7.636 3.143
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.348 0.175 198.6
48: (ns/day) (hour/ns)
48: Performance: 8.379 2.864
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.356 0.179 199.0
48: (ns/day) (hour/ns)
48: Performance: 8.207 2.924
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.346 0.174 199.0
48: (ns/day) (hour/ns)
48: Performance: 8.452 2.840
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.323 0.162 198.9
48: (ns/day) (hour/ns)
48: Performance: 9.043 2.654
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.372 0.187 198.7
48: (ns/day) (hour/ns)
48: Performance: 7.855 3.055
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
48: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (20589 ms)
48: [----------] 8 tests from PropagatorsWithConstraints/PeriodicActionsTest (167141 ms total)
48:
48: [----------] Global test environment tear-down
48: [==========] 27 tests from 3 test cases ran. (195227 ms total)
48: [ PASSED ] 27 tests.
48/52 Test #48: MdrunMpiCoordinationTestsTwoRanks ... Passed 195.31 sec
test 49
Start 49: GmxapiExternalInterfaceTests
49: Test command: /<<PKGBUILDDIR>>/build/basic/bin/gmxapi-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/GmxapiExternalInterfaceTests.xml"
49: Test timeout computed to be: 600
49: [==========] Running 9 tests from 2 test cases.
49: [----------] Global test environment set-up.
49: [----------] 8 tests from GmxApiTest
49: [ RUN ] GmxApiTest.ApiRunnerRestrainedMD
49: Setting the LD random seed to -938790422
49: Generated 331705 of the 331705 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 331705 of the 331705 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Excluding 3 bonded neighbours molecule type 'methane'
49:
49: NOTE 1 [file spc_and_methane.top, line 33]:
49: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
49: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
49: the time step of 2.0e-03 ps.
49: Maybe you forgot to change the constraints mdp option.
49:
49: Number of degrees of freedom in T-Coupling group System is 18.00
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
49: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
49:
49: Using 1 MPI thread
49: Using 2 OpenMP threads
49:
49:
49: NOTE: The number of threads is not equal to the number of (logical) cores
49: and the -pin option is set to auto: will not pin threads to cores.
49: This can lead to significant performance degradation.
49: Consider using -pin on (and -pinoffset in case you run multiple jobs).
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Water and methane'
49: 2 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
49: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.392 0.196 199.7
49: (ns/day) (hour/ns)
49: Performance: 2.580 9.304
49: [ OK ] GmxApiTest.ApiRunnerRestrainedMD (3380 ms)
49: [ RUN ] GmxApiTest.SystemConstruction
49: Setting the LD random seed to -1083069819
49: Generated 331705 of the 331705 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 331705 of the 331705 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Excluding 3 bonded neighbours molecule type 'methane'
49:
49: NOTE 1 [file spc_and_methane.top, line 33]:
49: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
49: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
49: the time step of 2.0e-03 ps.
49: Maybe you forgot to change the constraints mdp option.
49:
49: Number of degrees of freedom in T-Coupling group System is 18.00
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_SystemConstruction_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 2 notes
49: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
49: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49: [ OK ] GmxApiTest.SystemConstruction (3197 ms)
49: [ RUN ] GmxApiTest.SaneVersionComparisons
49: [ OK ] GmxApiTest.SaneVersionComparisons (0 ms)
49: [ RUN ] GmxApiTest.VersionNamed0_1_Features
49: [ OK ] GmxApiTest.VersionNamed0_1_Features (1 ms)
49: [ RUN ] GmxApiTest.RunnerBasicMD
49: Setting the LD random seed to 170446313
49: Generated 331705 of the 331705 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 331705 of the 331705 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Excluding 3 bonded neighbours molecule type 'methane'
49:
49: NOTE 1 [file spc_and_methane.top, line 33]:
49: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
49: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
49: the time step of 2.0e-03 ps.
49: Maybe you forgot to change the constraints mdp option.
49:
49: Number of degrees of freedom in T-Coupling group System is 18.00
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
49: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
49:
49: Using 1 MPI thread
49: Using 2 OpenMP threads
49:
49:
49: NOTE: The number of threads is not equal to the number of (logical) cores
49: and the -pin option is set to auto: will not pin threads to cores.
49: This can lead to significant performance degradation.
49: Consider using -pin on (and -pinoffset in case you run multiple jobs).
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Water and methane'
49: 2 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
49: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.369 0.185 199.7
49: (ns/day) (hour/ns)
49: Performance: 2.737 8.770
49: [ OK ] GmxApiTest.RunnerBasicMD (3401 ms)
49: [ RUN ] GmxApiTest.RunnerReinitialize
49: Setting the LD random seed to -2136798632
49: Generated 331705 of the 331705 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 331705 of the 331705 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Excluding 3 bonded neighbours molecule type 'methane'
49:
49: NOTE 1 [file spc_and_methane.top, line 33]:
49: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
49: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
49: the time step of 2.0e-03 ps.
49: Maybe you forgot to change the constraints mdp option.
49:
49: Number of degrees of freedom in T-Coupling group System is 18.00
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
49: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
49:
49: Using 1 MPI thread
49: Using 2 OpenMP threads
49:
49:
49: NOTE: The number of threads is not equal to the number of (logical) cores
49: and the -pin option is set to auto: will not pin threads to cores.
49: This can lead to significant performance degradation.
49: Consider using -pin on (and -pinoffset in case you run multiple jobs).
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Water and methane'
49: 20 steps, 0.0 ps.
49:
49:
49: Received the remote INT/TERM signal, stopping within 50 steps
49:
49: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
49: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.431 0.216 199.6
49: (ns/day) (hour/ns)
49: Performance: 16.393 1.464
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
49: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
49:
49: Using 1 MPI thread
49: Using 2 OpenMP threads
49:
49:
49: NOTE: The number of threads is not equal to the number of (logical) cores
49: and the -pin option is set to auto: will not pin threads to cores.
49: This can lead to significant performance degradation.
49: Consider using -pin on (and -pinoffset in case you run multiple jobs).
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Water and methane'
49: 20 steps, 0.0 ps.
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.454 0.228 199.4
49: (ns/day) (hour/ns)
49: Performance: 15.570 1.541
49: [ OK ] GmxApiTest.RunnerReinitialize (3667 ms)
49: [ RUN ] GmxApiTest.RunnerContinuedMD
49: Setting the LD random seed to -1402723918
49: Generated 331705 of the 331705 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 331705 of the 331705 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Excluding 3 bonded neighbours molecule type 'methane'
49:
49: NOTE 1 [file spc_and_methane.top, line 33]:
49: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
49: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
49: the time step of 2.0e-03 ps.
49: Maybe you forgot to change the constraints mdp option.
49:
49: Number of degrees of freedom in T-Coupling group System is 18.00
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerContinuedMD_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerContinuedMD.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
49: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
49:
49: Using 1 MPI thread
49: Using 2 OpenMP threads
49:
49:
49: NOTE: The number of threads is not equal to the number of (logical) cores
49: and the -pin option is set to auto: will not pin threads to cores.
49: This can lead to significant performance degradation.
49: Consider using -pin on (and -pinoffset in case you run multiple jobs).
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Water and methane'
49: 10 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
49: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.370 0.186 199.5
49: (ns/day) (hour/ns)
49: Performance: 10.001 2.400
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerContinuedMD.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
49: Overriding nsteps with value passed on the command line: 20 steps, 0.0391 ps
49: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
49:
49:
49: Using 1 MPI thread
49: Using 2 OpenMP threads
49:
49:
49: NOTE: The number of threads is not equal to the number of (logical) cores
49: and the -pin option is set to auto: will not pin threads to cores.
49: This can lead to significant performance degradation.
49: Consider using -pin on (and -pinoffset in case you run multiple jobs).
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Water and methane'
49: 20 steps, 0.0 ps.
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.434 0.218 199.4
49: (ns/day) (hour/ns)
49: Performance: 16.265 1.476
49: [ OK ] GmxApiTest.RunnerContinuedMD (3610 ms)
49: [ RUN ] GmxApiTest.ApiRunnerStopSignalClient
49: Setting the LD random seed to -378463021
49: Generated 331705 of the 331705 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 331705 of the 331705 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Excluding 3 bonded neighbours molecule type 'methane'
49:
49: NOTE 1 [file spc_and_methane.top, line 33]:
49: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
49: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
49: the time step of 2.0e-03 ps.
49: Maybe you forgot to change the constraints mdp option.
49:
49: Number of degrees of freedom in T-Coupling group System is 18.00
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
49: Changing nstlist from 10 to 1, rlist from 1.041 to 1
49:
49: Using 1 MPI thread
49: Using 2 OpenMP threads
49:
49:
49: NOTE: The number of threads is not equal to the number of (logical) cores
49: and the -pin option is set to auto: will not pin threads to cores.
49: This can lead to significant performance degradation.
49: Consider using -pin on (and -pinoffset in case you run multiple jobs).
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Water and methane'
49: 1 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
49: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.355 0.178 199.7
49: (ns/day) (hour/ns)
49: Performance: 1.896 12.655
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
49: Overriding nsteps with value passed on the command line: 2 steps, 0.00391 ps
49: Changing nstlist from 10 to 1, rlist from 1.041 to 1
49:
49:
49: Using 1 MPI thread
49: Using 2 OpenMP threads
49:
49:
49: NOTE: The number of threads is not equal to the number of (logical) cores
49: and the -pin option is set to auto: will not pin threads to cores.
49: This can lead to significant performance degradation.
49: Consider using -pin on (and -pinoffset in case you run multiple jobs).
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Water and methane'
49: 2 steps, 0.0 ps.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.371 0.186 199.5
49: (ns/day) (hour/ns)
49: Performance: 1.817 13.210
49: [ OK ] GmxApiTest.ApiRunnerStopSignalClient (3576 ms)
49: [----------] 8 tests from GmxApiTest (20835 ms total)
49:
49: [----------] 1 test from GmxApiBasicTest
49: [ RUN ] GmxApiBasicTest.Status
49: [ OK ] GmxApiBasicTest.Status (0 ms)
49: [----------] 1 test from GmxApiBasicTest (0 ms total)
49:
49: [----------] Global test environment tear-down
49: [==========] 9 tests from 2 test cases ran. (20837 ms total)
49: [ PASSED ] 9 tests.
49/52 Test #49: GmxapiExternalInterfaceTests ........ Passed 20.91 sec
test 50
Start 50: GmxapiMpiTests
50: Test command: /<<PKGBUILDDIR>>/build/basic/bin/gmxapi-mpi-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/GmxapiMpiTests.xml"
50: Test timeout computed to be: 600
50: [==========] Running 9 tests from 2 test cases.
50: [----------] Global test environment set-up.
50: [----------] 8 tests from GmxApiTest
50: [ RUN ] GmxApiTest.ApiRunnerRestrainedMD
50: Setting the LD random seed to 245581227
50: Generated 331705 of the 331705 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 331705 of the 331705 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Excluding 3 bonded neighbours molecule type 'methane'
50:
50: NOTE 1 [file spc_and_methane.top, line 33]:
50: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
50: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
50: the time step of 2.0e-03 ps.
50: Maybe you forgot to change the constraints mdp option.
50:
50: Number of degrees of freedom in T-Coupling group System is 18.00
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
50: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
50:
50: Using 1 MPI thread
50: Using 2 OpenMP threads
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Water and methane'
50: 2 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
50: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.382 0.191 199.7
50: (ns/day) (hour/ns)
50: Performance: 2.645 9.075
50: [ OK ] GmxApiTest.ApiRunnerRestrainedMD (3367 ms)
50: [ RUN ] GmxApiTest.SystemConstruction
50: Setting the LD random seed to -1980461713
50: Generated 331705 of the 331705 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 331705 of the 331705 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Excluding 3 bonded neighbours molecule type 'methane'
50:
50: NOTE 1 [file spc_and_methane.top, line 33]:
50: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
50: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
50: the time step of 2.0e-03 ps.
50: Maybe you forgot to change the constraints mdp option.
50:
50: Number of degrees of freedom in T-Coupling group System is 18.00
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_SystemConstruction_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 2 notes
50: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
50: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50: [ OK ] GmxApiTest.SystemConstruction (3189 ms)
50: [ RUN ] GmxApiTest.SaneVersionComparisons
50: [ OK ] GmxApiTest.SaneVersionComparisons (0 ms)
50: [ RUN ] GmxApiTest.VersionNamed0_1_Features
50: [ OK ] GmxApiTest.VersionNamed0_1_Features (0 ms)
50: [ RUN ] GmxApiTest.RunnerBasicMD
50: Setting the LD random seed to -1525646856
50: Generated 331705 of the 331705 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 331705 of the 331705 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Excluding 3 bonded neighbours molecule type 'methane'
50:
50: NOTE 1 [file spc_and_methane.top, line 33]:
50: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
50: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
50: the time step of 2.0e-03 ps.
50: Maybe you forgot to change the constraints mdp option.
50:
50: Number of degrees of freedom in T-Coupling group System is 18.00
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
50: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
50:
50: Using 1 MPI thread
50: Using 2 OpenMP threads
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Water and methane'
50: 2 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
50: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.669 0.335 199.8
50: (ns/day) (hour/ns)
50: Performance: 1.511 15.883
50: [ OK ] GmxApiTest.RunnerBasicMD (3552 ms)
50: [ RUN ] GmxApiTest.RunnerReinitialize
50: Setting the LD random seed to 1514458704
50: Generated 331705 of the 331705 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 331705 of the 331705 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Excluding 3 bonded neighbours molecule type 'methane'
50:
50: NOTE 1 [file spc_and_methane.top, line 33]:
50: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
50: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
50: the time step of 2.0e-03 ps.
50: Maybe you forgot to change the constraints mdp option.
50:
50: Number of degrees of freedom in T-Coupling group System is 18.00
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
50: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
50:
50: Using 1 MPI thread
50: Using 2 OpenMP threads
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Water and methane'
50: 20 steps, 0.0 ps.
50:
50:
50: Received the remote INT/TERM signal, stopping within 50 steps
50:
50: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
50: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.554 0.278 199.7
50: (ns/day) (hour/ns)
50: Performance: 12.765 1.880
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
50: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
50:
50: Using 1 MPI thread
50: Using 2 OpenMP threads
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Water and methane'
50: 20 steps, 0.0 ps.
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.521 0.261 199.5
50: (ns/day) (hour/ns)
50: Performance: 13.557 1.770
50: [ OK ] GmxApiTest.RunnerReinitialize (3754 ms)
50: [ RUN ] GmxApiTest.RunnerContinuedMD
50: Setting the LD random seed to -468358082
50: Generated 331705 of the 331705 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 331705 of the 331705 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Excluding 3 bonded neighbours molecule type 'methane'
50:
50: NOTE 1 [file spc_and_methane.top, line 33]:
50: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
50: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
50: the time step of 2.0e-03 ps.
50: Maybe you forgot to change the constraints mdp option.
50:
50: Number of degrees of freedom in T-Coupling group System is 18.00
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerContinuedMD_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerContinuedMD.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
50: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
50:
50: Using 1 MPI thread
50: Using 2 OpenMP threads
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Water and methane'
50: 10 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
50: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.424 0.213 199.6
50: (ns/day) (hour/ns)
50: Performance: 8.732 2.748
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerContinuedMD.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
50: Overriding nsteps with value passed on the command line: 20 steps, 0.0391 ps
50: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
50:
50:
50: Using 1 MPI thread
50: Using 2 OpenMP threads
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Water and methane'
50: 20 steps, 0.0 ps.
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.435 0.218 199.4
50: (ns/day) (hour/ns)
50: Performance: 16.236 1.478
50: [ OK ] GmxApiTest.RunnerContinuedMD (3647 ms)
50: [ RUN ] GmxApiTest.ApiRunnerStopSignalClient
50: Setting the LD random seed to -1606352987
50: Generated 331705 of the 331705 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 331705 of the 331705 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Excluding 3 bonded neighbours molecule type 'methane'
50:
50: NOTE 1 [file spc_and_methane.top, line 33]:
50: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
50: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
50: the time step of 2.0e-03 ps.
50: Maybe you forgot to change the constraints mdp option.
50:
50: Number of degrees of freedom in T-Coupling group System is 18.00
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
50: Changing nstlist from 10 to 1, rlist from 1.041 to 1
50:
50: Using 1 MPI thread
50: Using 2 OpenMP threads
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Water and methane'
50: 1 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
50: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.381 0.191 199.7
50: (ns/day) (hour/ns)
50: Performance: 1.768 13.572
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2020.3-Raspbian-2020.3-1 (single precision)
50: Overriding nsteps with value passed on the command line: 2 steps, 0.00391 ps
50: Changing nstlist from 10 to 1, rlist from 1.041 to 1
50:
50:
50: Using 1 MPI thread
50: Using 2 OpenMP threads
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Water and methane'
50: 2 steps, 0.0 ps.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.370 0.186 199.6
50: (ns/day) (hour/ns)
50: Performance: 1.818 13.199
50: [ OK ] GmxApiTest.ApiRunnerStopSignalClient (3565 ms)
50: [----------] 8 tests from GmxApiTest (21077 ms total)
50:
50: [----------] 1 test from GmxApiBasicTest
50: [ RUN ] GmxApiBasicTest.Status
50: [ OK ] GmxApiBasicTest.Status (0 ms)
50: [----------] 1 test from GmxApiBasicTest (0 ms total)
50:
50: [----------] Global test environment tear-down
50: [==========] 9 tests from 2 test cases ran. (21078 ms total)
50: [ PASSED ] 9 tests.
50/52 Test #50: GmxapiMpiTests ...................... Passed 21.15 sec
test 51
Start 51: GmxapiInternalInterfaceTests
51: Test command: /<<PKGBUILDDIR>>/build/basic/bin/workflow-details-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/GmxapiInternalInterfaceTests.xml"
51: Test timeout computed to be: 600
51: [==========] Running 2 tests from 1 test case.
51: [----------] Global test environment set-up.
51: [----------] 2 tests from GmxApiTest
51: [ RUN ] GmxApiTest.BuildApiWorkflowImpl
51: Setting the LD random seed to -1842235152
51: Generated 331705 of the 331705 non-bonded parameter combinations
51: Generating 1-4 interactions: fudge = 0.5
51: Generated 331705 of the 331705 1-4 parameter combinations
51: Excluding 2 bonded neighbours molecule type 'SOL'
51: Excluding 3 bonded neighbours molecule type 'methane'
51:
51: NOTE 1 [file spc_and_methane.top, line 33]:
51: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
51: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
51: the time step of 2.0e-03 ps.
51: Maybe you forgot to change the constraints mdp option.
51:
51: Number of degrees of freedom in T-Coupling group System is 18.00
51:
51: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests/Testing/Temporary/GmxApiTest_BuildApiWorkflowImpl_input.mdp]:
51: You are using a plain Coulomb cut-off, which might produce artifacts.
51: You might want to consider using PME electrostatics.
51:
51:
51:
51: There were 2 notes
51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
51: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
51: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
51: Note that mdrun will redetermine rlist based on the actual pair-list setup
51: This run will generate roughly 0 Mb of data
51: [ OK ] GmxApiTest.BuildApiWorkflowImpl (3110 ms)
51: [ RUN ] GmxApiTest.CreateApiWorkflow
51: Setting the LD random seed to 1425598890
51: Generated 331705 of the 331705 non-bonded parameter combinations
51: Generating 1-4 interactions: fudge = 0.5
51: Generated 331705 of the 331705 1-4 parameter combinations
51: Excluding 2 bonded neighbours molecule type 'SOL'
51: Excluding 3 bonded neighbours molecule type 'methane'
51:
51: NOTE 1 [file spc_and_methane.top, line 33]:
51: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
51: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
51: the time step of 2.0e-03 ps.
51: Maybe you forgot to change the constraints mdp option.
51:
51: Number of degrees of freedom in T-Coupling group System is 18.00
51:
51: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests/Testing/Temporary/GmxApiTest_CreateApiWorkflow_input.mdp]:
51: You are using a plain Coulomb cut-off, which might produce artifacts.
51: You might want to consider using PME electrostatics.
51:
51:
51:
51: There were 2 notes
51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
51: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
51: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
51: Note that mdrun will redetermine rlist based on the actual pair-list setup
51: This run will generate roughly 0 Mb of data
51: [ OK ] GmxApiTest.CreateApiWorkflow (3091 ms)
51: [----------] 2 tests from GmxApiTest (6201 ms total)
51:
51: [----------] Global test environment tear-down
51: [==========] 2 tests from 1 test case ran. (6202 ms total)
51: [ PASSED ] 2 tests.
51/52 Test #51: GmxapiInternalInterfaceTests ........ Passed 6.27 sec
test 52
Start 52: GmxapiInternalsMpiTests
52: Test command: /<<PKGBUILDDIR>>/build/basic/bin/workflow-details-mpi-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/GmxapiInternalsMpiTests.xml"
52: Test timeout computed to be: 600
52: [==========] Running 2 tests from 1 test case.
52: [----------] Global test environment set-up.
52: [----------] 2 tests from GmxApiTest
52: [ RUN ] GmxApiTest.BuildApiWorkflowImpl
52: Setting the LD random seed to 1588396016
52: Generated 331705 of the 331705 non-bonded parameter combinations
52: Generating 1-4 interactions: fudge = 0.5
52: Generated 331705 of the 331705 1-4 parameter combinations
52: Excluding 2 bonded neighbours molecule type 'SOL'
52: Excluding 3 bonded neighbours molecule type 'methane'
52:
52: NOTE 1 [file spc_and_methane.top, line 33]:
52: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
52: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
52: the time step of 2.0e-03 ps.
52: Maybe you forgot to change the constraints mdp option.
52:
52: Number of degrees of freedom in T-Coupling group System is 18.00
52:
52: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests/Testing/Temporary/GmxApiTest_BuildApiWorkflowImpl_input.mdp]:
52: You are using a plain Coulomb cut-off, which might produce artifacts.
52: You might want to consider using PME electrostatics.
52:
52:
52:
52: There were 2 notes
52: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
52: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
52: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
52: Note that mdrun will redetermine rlist based on the actual pair-list setup
52: This run will generate roughly 0 Mb of data
52: [ OK ] GmxApiTest.BuildApiWorkflowImpl (3113 ms)
52: [ RUN ] GmxApiTest.CreateApiWorkflow
52: Setting the LD random seed to -878161443
52: Generated 331705 of the 331705 non-bonded parameter combinations
52: Generating 1-4 interactions: fudge = 0.5
52: Generated 331705 of the 331705 1-4 parameter combinations
52: Excluding 2 bonded neighbours molecule type 'SOL'
52: Excluding 3 bonded neighbours molecule type 'methane'
52:
52: NOTE 1 [file spc_and_methane.top, line 33]:
52: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
52: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
52: the time step of 2.0e-03 ps.
52: Maybe you forgot to change the constraints mdp option.
52:
52: Number of degrees of freedom in T-Coupling group System is 18.00
52:
52: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests/Testing/Temporary/GmxApiTest_CreateApiWorkflow_input.mdp]:
52: You are using a plain Coulomb cut-off, which might produce artifacts.
52: You might want to consider using PME electrostatics.
52:
52:
52:
52: There were 2 notes
52: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
52: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
52: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
52: Note that mdrun will redetermine rlist based on the actual pair-list setup
52: This run will generate roughly 0 Mb of data
52: [ OK ] GmxApiTest.CreateApiWorkflow (3097 ms)
52: [----------] 2 tests from GmxApiTest (6210 ms total)
52:
52: [----------] Global test environment tear-down
52: [==========] 2 tests from 1 test case ran. (6211 ms total)
52: [ PASSED ] 2 tests.
52/52 Test #52: GmxapiInternalsMpiTests ............. Passed 6.28 sec
100% tests passed, 0 tests failed out of 52
Label Time Summary:
GTest = 814.90 sec*proc (52 tests)
IntegrationTest = 356.28 sec*proc (9 tests)
MpiTest = 567.21 sec*proc (8 tests)
SlowTest = 386.87 sec*proc (2 tests)
UnitTest = 71.75 sec*proc (41 tests)
Total Test time (real) = 815.37 sec
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/external/googletest/googlemock && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_CAN_STREAM_RESULTS=0 -DGTEST_CREATE_SHARED_LIBRARY=1 -D_GNU_SOURCE=1 -Dgmock_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -I/<<PKGBUILDDIR>>/src/external/googletest/googlemock -I/<<PKGBUILDDIR>>/src/external/googletest/googletest -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wshadow -DGTEST_HAS_PTHREAD=1 -fexceptions -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -Wno-deprecated-copy -std=c++14 -o CMakeFiles/gmock.dir/src/gmock-all.cc.o -c /<<PKGBUILDDIR>>/src/external/googletest/googlemock/src/gmock-all.cc
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/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgmock.so -o ../../../../lib/libgmock.so CMakeFiles/gmock.dir/src/gmock-all.cc.o -lpthread ../../../../lib/libgtest.so -lpthread
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/cmdlinetest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/cmdlinetest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/conftest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/conftest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/filematchers.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/filematchers.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/interactivetest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/interactivetest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/loggertest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/loggertest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/mpi_printer.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/mpi_printer.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/mpitest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/mpitest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/refdata.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/refdata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/refdata_xml.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/refdata_xml.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/simulationdatabase.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/simulationdatabase.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/stdiohelper.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/stdiohelper.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/stringtest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/stringtest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/testasserts.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/testasserts.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/testfilemanager.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/testfilemanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/testfileredirector.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/testfileredirector.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/testinit.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/testinit.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/testmatchers.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/testmatchers.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/testoptions.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/testoptions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/textblockmatchers.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/textblockmatchers.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/tprfilegenerator.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tprfilegenerator.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/__/external/tinyxml2/tinyxml2.cpp.o -c /<<PKGBUILDDIR>>/src/external/tinyxml2/tinyxml2.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/physicalnodecommunicator_mpi.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/energyreader.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/energyreader.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/energycomparison.cpp
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/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -o ../../../bin/testutils-mpi-test ../../../lib/libtestutils.a ../../../lib/libgromacs_d.so.5.0.0 ../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/utility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
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cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/utility/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/CMakeFiles/utility-test.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/moduletest.cpp
Scanning dependencies of target utility-test
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/alignedallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/alignedallocator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-test.dir/refdata_tests.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tests/refdata_tests.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdlib-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/calc_verletbuf.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/mdmodulenotification.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/mdmodulenotification.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/constr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/terminationhelper.cpp
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:54:
/usr/include/c++/9/bits/stl_vector.h: In function 'std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/stl_vector.h:622:7: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
622 | vector(initializer_list<value_type> __l,
| ^~~~~~
/usr/include/c++/9/bits/stl_vector.h: In function 'std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/9/bits/stl_vector.h:622:7: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_vector.h: In function 'std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/9/bits/stl_vector.h:622:7: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/trajectorycomparison.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp: In member function 'virtual void gmx::test::{anonymous}::ConstraintsTest_SingleConstraint_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:331:51: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
331 | std::vector<real> masses = { 1.0, 12.0 };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:333:45: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
333 | std::vector<real> constraintsR0 = { 0.1 };
| ^
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tests/testasserts_tests.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp: In member function 'virtual void gmx::test::{anonymous}::ConstraintsTest_TwoDisjointConstraints_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:377:67: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
377 | std::vector<real> masses = { 0.5, 1.0 / 3.0, 0.25, 1.0 };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:379:50: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
379 | std::vector<real> constraintsR0 = { 2.0, 1.0 };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:384:5: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
384 | };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:388:5: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
388 | };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:390:104: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
390 | std::vector<RVec> v = { { 0.0, 1.0, 0.0 }, { 1.0, 0.0, 0.0 }, { 0.0, 0.0, 1.0 }, { 0.0, 0.0, 0.0 } };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp: In member function 'virtual void gmx::test::{anonymous}::ConstraintsTest_ThreeSequentialConstraints_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:431:50: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
431 | std::vector<real> constraintsR0 = { 0.1, 0.2 };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:438:104: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
438 | { twoTenthsOverSqrtThree, twoTenthsOverSqrtThree, twoTenthsOverSqrtThree } };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:440:101: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
440 | std::vector<RVec> xPrime = { { 0.08, 0.07, 0.01 }, { -0.02, 0.01, -0.02 }, { 0.10, 0.12, 0.11 } };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:442:85: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
442 | std::vector<RVec> v = { { 1.0, 0.0, 0.0 }, { 0.0, 1.0, 0.0 }, { 0.0, 0.0, 1.0 } };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp: In member function 'virtual void gmx::test::{anonymous}::ConstraintsTest_ThreeConstraintsWithCentralAtom_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:481:61: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
481 | std::vector<real> masses = { 12.0, 1.0, 1.0, 1.0 };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:483:45: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
483 | std::vector<real> constraintsR0 = { 0.1 };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:488:5: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
488 | };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:493:59: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
493 | { -0.005, 0.011, 0.102 } };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:495:104: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
495 | std::vector<RVec> v = { { 1.0, 0.0, 0.0 }, { 1.0, 0.0, 0.0 }, { 1.0, 0.0, 0.0 }, { 1.0, 0.0, 0.0 } };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp: In member function 'virtual void gmx::test::{anonymous}::ConstraintsTest_FourSequentialConstraints_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:534:67: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
534 | std::vector<real> masses = { 0.5, 1.0 / 3.0, 0.25, 1.0 };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:541:5: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
541 | };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:545:5: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
545 | };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:547:106: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
547 | std::vector<RVec> v = { { 0.0, 0.0, 2.0 }, { 0.0, 0.0, 3.0 }, { 0.0, 0.0, -4.0 }, { 0.0, 0.0, -1.0 } };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp: In member function 'virtual void gmx::test::{anonymous}::ConstraintsTest_TriangleOfConstraints_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:594:63: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
594 | { 0.0, 0.0, oneTenthOverSqrtTwo } };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:596:103: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
596 | std::vector<RVec> xPrime = { { 0.09, -0.02, 0.01 }, { -0.02, 0.10, -0.02 }, { 0.03, -0.01, 0.07 } };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:598:88: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
598 | std::vector<RVec> v = { { 1.0, 1.0, 1.0 }, { -2.0, -2.0, -2.0 }, { 1.0, 1.0, 1.0 } };
| ^
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/arrayref.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/arrayref.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tests/xvgtest_tests.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestdata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/trajectoryreader.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/trajectoryreader.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestdata.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestdata.cpp:50:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestdata.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestdata.cpp:50:
/usr/include/c++/9/bits/stl_vector.h: In constructor 'gmx::test::ConstraintsTestData::ConstraintsTestData(const string&, int, std::vector<double>, std::vector<int>, std::vector<double>, bool, real (*)[3], bool, float, real, real, const std::vector<gmx::BasicVector<double> >&, const std::vector<gmx::BasicVector<double> >&, const std::vector<gmx::BasicVector<double> >&, real, gmx_bool, int, int, real)':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/testutils-test.dir/interactivetest.cpp.o CMakeFiles/testutils-test.dir/refdata_tests.cpp.o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -o ../../../bin/testutils-test ../../../lib/libtestutils.a ../../../lib/libgromacs_d.so.5.0.0 ../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -P CMakeFiles/mdrun_test_infrastructure.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun_test_infrastructure.dir/link.txt --verbose=1
/usr/bin/ar qc ../../../../lib/libmdrun_test_infrastructure.a CMakeFiles/mdrun_test_infrastructure.dir/energyreader.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/mdmodulenotification.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/trajectoryreader.cpp.o
/usr/bin/ranlib ../../../../lib/libmdrun_test_infrastructure.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 70%] Built target mdrun_test_infrastructure
/usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/applied_forces/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/DependInfo.cmake --color=
Scanning dependencies of target applied_forces-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/densityfitting.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/tests/densityfitting.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 71%] Built target testutils-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/bitmask32.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/bitmask32.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestrunners.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/ebin.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/ebin.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/densityfittingoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/tests/densityfittingoptions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/densityfittingamplitudelookup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/tests/densityfittingamplitudelookup.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/energyoutput.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/energyoutput.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/bitmask64.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/bitmask64.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/electricfield.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/tests/electricfield.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/bitmask128.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/bitmask128.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/leapfrog.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrog.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/tests/electricfield.cpp:46:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/tests/electricfield.cpp:46:
/usr/include/c++/9/bits/stl_vector.h: In function 'void gmx::test::{anonymous}::ElectricFieldTest::test(int, real, real, real, real, real)':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build.make src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/listed_forces/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/DependInfo.cmake --color=
Scanning dependencies of target listed_forces-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build.make src/gromacs/listed_forces/tests/CMakeFiles/listed_forces-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/listed_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/listed_forces-test.dir/bonded.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/applied_forces-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/applied_forces-test.dir/densityfitting.cpp.o CMakeFiles/applied_forces-test.dir/densityfittingoptions.cpp.o CMakeFiles/applied_forces-test.dir/densityfittingamplitudelookup.cpp.o CMakeFiles/applied_forces-test.dir/electricfield.cpp.o CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/applied_forces-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 72%] Built target applied_forces-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/cstringutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/cstringutil.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/listed_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/listed_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:62,
from /<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:51:
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h: In function 'testing::internal::ParamGenerator<typename testing::internal::IteratorTraits<Iterator>::value_type> testing::ValuesIn(ForwardIterator, ForwardIterator) [with ForwardIterator = __gnu_cxx::__normal_iterator<const gmx::{anonymous}::iListInput*, std::vector<gmx::{anonymous}::iListInput> >]':
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h:310:1: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::{anonymous}::iListInput*, std::vector<gmx::{anonymous}::iListInput> >' changed in GCC 7.1
310 | ValuesIn(ForwardIterator begin, ForwardIterator end) {
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h:310:1: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::{anonymous}::iListInput*, std::vector<gmx::{anonymous}::iListInput> >' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:51:
/usr/include/c++/9/bits/stl_vector.h: In function 'std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = gmx::{anonymous}::iListInput; _Alloc = std::allocator<gmx::{anonymous}::iListInput>]':
/usr/include/c++/9/bits/stl_vector.h:622:7: note: parameter passing for argument of type 'std::initializer_list<gmx::{anonymous}::iListInput>' changed in GCC 7.1
622 | vector(initializer_list<value_type> __l,
| ^~~~~~
/usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/DependInfo.cmake --color=
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.cpp:43:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_grp_tcstat&}; _Tp = t_grp_tcstat; _Alloc = std::allocator<t_grp_tcstat>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_grp_tcstat>::iterator' {aka '__gnu_cxx::__normal_iterator<t_grp_tcstat*, std::vector<t_grp_tcstat> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
Scanning dependencies of target onlinehelp-test-shared
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/mock_helptopic.cpp
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In constructor 'std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/9/bits/stl_vector.h:622:7: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:62,
from /<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:51:
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h: In function 'testing::internal::ParamGenerator<std::tuple<gmx::{anonymous}::iListInput, std::vector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > >, int> > gmx::{anonymous}::gtest_RestraintsListedForcesTest_EvalGenerator_()':
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h:325:53: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::{anonymous}::iListInput*, std::vector<gmx::{anonymous}::iListInput> >' changed in GCC 7.1
325 | return ValuesIn(container.begin(), container.end());
| ^
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h: In function 'testing::internal::ParamGenerator<std::tuple<gmx::{anonymous}::iListInput, std::vector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > >, int> > gmx::{anonymous}::gtest_PolarizeListedForcesTest_EvalGenerator_()':
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h:325:53: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::{anonymous}::iListInput*, std::vector<gmx::{anonymous}::iListInput> >' changed in GCC 7.1
325 | return ValuesIn(container.begin(), container.end());
| ^
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h: In function 'testing::internal::ParamGenerator<std::tuple<gmx::{anonymous}::iListInput, std::vector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > >, int> > gmx::{anonymous}::gtest_DihedralListedForcesTest_EvalGenerator_()':
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h:325:53: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::{anonymous}::iListInput*, std::vector<gmx::{anonymous}::iListInput> >' changed in GCC 7.1
325 | return ValuesIn(container.begin(), container.end());
| ^
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h: In function 'testing::internal::ParamGenerator<std::tuple<gmx::{anonymous}::iListInput, std::vector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > >, int> > gmx::{anonymous}::gtest_AngleListedForcesTest_EvalGenerator_()':
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h:325:53: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::{anonymous}::iListInput*, std::vector<gmx::{anonymous}::iListInput> >' changed in GCC 7.1
325 | return ValuesIn(container.begin(), container.end());
| ^
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.cpp:43:
/usr/include/c++/9/bits/stl_vector.h: In constructor 'gmx::test::LeapFrogTestData::LeapFrogTestData(int, real, const real*, const real*, int, int)':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.cpp:43:
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_grp_tcstat*, std::vector<t_grp_tcstat> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_grp_tcstat*, std::vector<t_grp_tcstat> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h: In function 'testing::internal::ParamGenerator<std::tuple<gmx::{anonymous}::iListInput, std::vector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > >, int> > gmx::{anonymous}::gtest_BondListedForcesTest_EvalGenerator_()':
/<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest-param-test.h:325:53: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::{anonymous}::iListInput*, std::vector<gmx::{anonymous}::iListInput> >' changed in GCC 7.1
325 | return ValuesIn(container.begin(), container.end());
| ^
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp: In function 'void __static_initialization_and_destruction_0(int, int)':
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:590:25: note: parameter passing for argument of type 'std::initializer_list<gmx::{anonymous}::iListInput>' changed in GCC 7.1
590 | std::vector<iListInput> c_InputBonds = {
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:605:25: note: parameter passing for argument of type 'std::initializer_list<gmx::{anonymous}::iListInput>' changed in GCC 7.1
605 | std::vector<iListInput> c_InputAngles = {
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:629:25: note: parameter passing for argument of type 'std::initializer_list<gmx::{anonymous}::iListInput>' changed in GCC 7.1
629 | std::vector<iListInput> c_InputDihs = {
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:639:25: note: parameter passing for argument of type 'std::initializer_list<gmx::{anonymous}::iListInput>' changed in GCC 7.1
639 | std::vector<iListInput> c_InputPols = {
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:647:25: note: parameter passing for argument of type 'std::initializer_list<gmx::{anonymous}::iListInput>' changed in GCC 7.1
647 | std::vector<iListInput> c_InputRestraints = {
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:657:37: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
657 | std::vector<std::vector<gmx::RVec>> c_coordinatesForTests = {
| ^~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:657:37: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/listed_forces/tests/bonded.cpp:657:37: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestrunners.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestrunners.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestrunners.cpp:43:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestrunners.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestrunners.cpp:43:
/usr/include/c++/9/bits/stl_vector.h: In function 'void gmx::test::integrateLeapFrogSimple(gmx::test::LeapFrogTestData*, int)':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/cmake -P CMakeFiles/onlinehelp-test-shared.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test-shared.dir/link.txt --verbose=1
/usr/bin/ar qc ../../../../lib/libonlinehelp-test-shared.a CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o
/usr/bin/ranlib ../../../../lib/libonlinehelp-test-shared.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 72%] Built target onlinehelp-test-shared
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/defaultinitializationallocator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/settle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settle.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/listed_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/listed_forces-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/listed_forces-test.dir/bonded.cpp.o CMakeFiles/listed_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/listed_forces-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 72%] Built target listed_forces-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/enumerationhelpers.cpp
/usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/domdec/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/DependInfo.cmake --color=
Scanning dependencies of target domdec-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/domdec-test.dir/hashedmap.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/tests/hashedmap.cpp
/usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/ewald/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/DependInfo.cmake --color=
Scanning dependencies of target ewald-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmebsplinetest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/tests/localatomsetmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/settletestdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settletestdata.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settletestdata.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settletestdata.cpp:45:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_iparams&}; _Tp = t_iparams; _Alloc = std::allocator<t_iparams>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_iparams>::iterator' {aka '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settletestdata.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settletestdata.cpp:45:
/usr/include/c++/9/bits/stl_vector.h: In constructor 'gmx::test::SettleTestData::SettleTestData(int)':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settletestrunners.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/domdec-test.dir/hashedmap.cpp.o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/domdec-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 72%] Built target domdec-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp
/usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/fft/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fft/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fft/tests/CMakeFiles/fft-test.dir/DependInfo.cmake --color=
Scanning dependencies of target fft-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fft/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fft/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fft-test.dir/fft.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/tests/fft.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/shake.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/shake.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/topology/block.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/shake.cpp:37:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In function 'std::vector<double> gmx::{anonymous}::computeDisplacements(const std::vector<int>&, const std::vector<double>&)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ShakeTest::SetUp()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In function 'void gmx::{anonymous}::ShakeTest::runTest(size_t, size_t, const std::vector<int>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/fixedcapacityvector.cpp
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/internal/gtest-port.h:279,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/internal/gtest-linked_ptr.h:74,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-port.h:53,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-generated-internal-utils.h:44,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-internal-utils.h:45,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock-actions.h:46,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp:47:
/usr/include/c++/9/bits/stl_vector.h: In constructor 'std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/stl_vector.h:622:7: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
622 | vector(initializer_list<value_type> __l,
| ^~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ShakeTest_ConstrainsOneBond_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ShakeTest_ConstrainsTwoDisjointBonds_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ShakeTest_ConstrainsTwoBondsWithACommonAtom_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ShakeTest_ConstrainsThreeBondsWithCommonAtoms_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/internal/gtest-port.h:279,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/internal/gtest-linked_ptr.h:74,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-port.h:53,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-generated-internal-utils.h:44,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-internal-utils.h:45,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock-actions.h:46,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp:47:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/simulationsignal.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fft/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fft/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/internal/gtest-port.h:279,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/internal/gtest-linked_ptr.h:74,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-port.h:53,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-generated-internal-utils.h:44,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-internal-utils.h:45,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock-actions.h:46,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp:47:
/usr/include/c++/9/bits/stl_vector.h: In static member function 'static void gmx::test::{anonymous}::PmeGatherTest::SetUpTestCase()':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fft/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fft-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/fft-test.dir/fft.cpp.o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/fft-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 72%] Built target fft-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/inmemoryserializer.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/keyvaluetreeserializer.cpp
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp: In function 'void __static_initialization_and_destruction_0(int, int)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp:79:80: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
79 | 2.86F, 0.24F, 5.76F, 5.19F, 0.72F };
| ^
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp:118:1: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
118 | };
| ^
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp:146:1: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
146 | };
| ^
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/updategroups.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroups.cpp
/usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/DependInfo.cmake --color=
Scanning dependencies of target gpu_utils-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/gputest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/gputest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesolvetest.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroups.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroups.cpp:44:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_iparams&}; _Tp = t_iparams; _Alloc = std::allocator<t_iparams>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_iparams>::iterator' {aka '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroups.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroups.cpp:44:
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_ethane_Test::TestBody()':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_butaneUA_Test::TestBody()':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/clfftinitializer.cpp
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_waterFourSite_Test::TestBody()':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_methane_Test::TestBody()':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_ethaneUA_Test::TestBody()':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_waterThreeSite_Test::TestBody()':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_twoMoltypes_Test::TestBody()':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_waterFlexAngle_Test::TestBody()':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroupscog.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/keyvaluetreetransform.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroupscog.cpp:37:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_iparams&}; _Tp = t_iparams; _Alloc = std::allocator<t_iparams>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_iparams>::iterator' {aka '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroupscog.cpp:37:
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroupsCog_ComputesCogs_Test::TestBody()':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroupscog.cpp:137:28: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
137 | updateGroupsCog.addCogs(globalAtomIndices, positions);
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroupscog.cpp:137:28: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdlib-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o CMakeFiles/mdlib-test.dir/constr.cpp.o CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o CMakeFiles/mdlib-test.dir/ebin.cpp.o CMakeFiles/mdlib-test.dir/energyoutput.cpp.o CMakeFiles/mdlib-test.dir/leapfrog.cpp.o CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o CMakeFiles/mdlib-test.dir/settle.cpp.o CMakeFiles/mdlib-test.dir/settletestdata.cpp.o CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o CMakeFiles/mdlib-test.dir/shake.cpp.o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o CMakeFiles/mdlib-test.dir/updategroups.cpp.o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdlib-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 73%] Built target mdlib-test
/usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/hardware/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/hardware/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/DependInfo.cmake --color=
Scanning dependencies of target hardware-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/hardware/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/tests/hardwaretopology.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/logger.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/logger.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesplinespreadtest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/hardware/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/mutex.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/mutex.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/hardware/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/hardware-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/hardware-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 73%] Built target hardware-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/devicetransfers.cpp
/usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/math/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/CMakeFiles/math-test.dir/DependInfo.cmake --color=
Scanning dependencies of target math-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/arrayrefwithpadding.cpp
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/internal/gtest-port.h:279,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/internal/gtest-linked_ptr.h:74,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-port.h:53,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-generated-internal-utils.h:44,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-internal-utils.h:45,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock-actions.h:46,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesplinespreadtest.cpp:47:
/usr/include/c++/9/bits/stl_vector.h: In constructor 'std::vector<_Tp, _Alloc>::vector(_InputIterator, _InputIterator, const allocator_type&) [with _InputIterator = __gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >; <template-parameter-2-2> = void; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/9/bits/stl_vector.h:650:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
650 | vector(_InputIterator __first, _InputIterator __last,
| ^~~~~~
/usr/include/c++/9/bits/stl_vector.h:650:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesplinespreadtest.cpp: In function 'void __static_initialization_and_destruction_0(int, int)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesplinespreadtest.cpp:325:81: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
325 | c_sampleCoordinatesFull.begin() + 1);
| ^
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesplinespreadtest.cpp:328:81: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
328 | c_sampleCoordinatesFull.begin() + 3);
| ^
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesplinespreadtest.cpp:331:83: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
331 | c_sampleCoordinatesFull.begin() + 16);
| ^
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/math/arrayrefwithpadding.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/arrayrefwithpadding.cpp:43:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/math/arrayrefwithpadding.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/arrayrefwithpadding.cpp:43:
/usr/include/c++/9/bits/stl_vector.h: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::ArrayRefWithPaddingTest_AssignFromPaddedVectorWorks_Test<gmx::ArrayRefWithPadding<double> >]':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::ArrayRefWithPaddingTest_ConstructFromPointersWorks_Test<gmx::ArrayRefWithPadding<double> >]':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/path.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/path.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmetestcommon.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:43:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::HostAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:43:
/usr/include/c++/9/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> >]':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'void gmx::test::HostAllocatorTestCopyable_VectorsWithDefaultHostAllocatorAlwaysWorks_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = double]':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:57:
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::compareViews(gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:94:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
94 | void compareViews(ArrayRef<T> input, ArrayRef<T> output)
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:94:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp: In function 'void gmx::test::runTest(const gmx_gpu_info_t&, gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:100:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
100 | void runTest(const gmx_gpu_info_t& gpuInfo, ArrayRef<T> input, ArrayRef<T> output)
| ^~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:100:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:43:
/usr/include/c++/9/bits/stl_vector.h: In member function 'void gmx::test::HostAllocatorTestCopyable_TransfersWithoutPinningWork_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = double]':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:206:12: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
206 | runTest(*this->gpuInfo_, makeArrayRef(input), makeArrayRef(output));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:206:12: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:206:12: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
In file included from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:57:
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::compareViews(gmx::ArrayRef<gmx::BasicVector<ValueType> >, gmx::ArrayRef<gmx::BasicVector<ValueType> >) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:105:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
105 | void compareViews(ArrayRef<BasicVector<T>> input, ArrayRef<BasicVector<T>> output)
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:105:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp: In function 'void gmx::test::runTest(const gmx_gpu_info_t&, gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = gmx::BasicVector<double>]':
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:100:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
100 | void runTest(const gmx_gpu_info_t& gpuInfo, ArrayRef<T> input, ArrayRef<T> output)
| ^~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:100:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:43:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/physicalnodecommunicator.cpp
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:43:
/usr/include/c++/9/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >]':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'void gmx::test::HostAllocatorTestCopyable_TransfersWithoutPinningWork_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::BasicVector<double>]':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:206:12: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
206 | runTest(*this->gpuInfo_, makeArrayRef(input), makeArrayRef(output));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:206:12: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:206:12: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:43:
/usr/include/c++/9/bits/stl_vector.h: In member function 'void gmx::test::HostAllocatorTestCopyable_VectorsWithDefaultHostAllocatorAlwaysWorks_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::BasicVector<double>]':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/coordinatetransformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmetestcommon.cpp: In function 'void gmx::test::pmeInitAtoms(gmx_pme_t*, gmx::StatePropagatorDataGpu*, gmx::test::CodePath, const CoordinatesVector&, const ChargesVector&)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmetestcommon.cpp:201:43: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
201 | stateGpu->copyCoordinatesToGpu(arrayRefFromArray(coordinates.data(), coordinates.size()),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
202 | gmx::AtomLocality::All);
| ~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/stringutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/stringutil.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/testhardwarecontexts.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/testhardwarecontexts.cpp
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp: In member function 'virtual void gmx::test::TranslateAndScaleTest_identityTransformation_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:77:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
77 | translateAndScale(toBeTransformed);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp: In member function 'virtual void gmx::test::TranslateAndScaleTest_translationWithIdentityScaling_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:84:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
84 | translateAndScale(testVectors_);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp: In member function 'virtual void gmx::test::TranslateAndScaleTest_scalingWithZeroTranslation_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:94:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
94 | translateAndScale(testVectors_);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp: In member function 'virtual void gmx::test::TranslateAndScaleTest_translationAndScalingNonTrivial_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:104:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
104 | translateAndScale(testVectors_);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp: In member function 'virtual void gmx::test::TranslateAndScaleTest_scalingIdentity_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:115:10: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
115 | scale(testVectors_);
| ~~~~~^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp: In member function 'virtual void gmx::test::TranslateAndScaleTest_scalingNonTrivial_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:125:10: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
125 | scale(testVectors_);
| ~~~~~^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ewald-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o CMakeFiles/ewald-test.dir/testhardwarecontexts.cpp.o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/ewald-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp: In member function 'virtual void gmx::test::TranslateAndScaleTest_scalingInverseNoZero_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:133:10: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
133 | scale(testVectors_);
| ~~~~~^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:134:35: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
134 | scale.inverseIgnoringZeroScale(testVectors_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp: In member function 'virtual void gmx::test::TranslateAndScaleTest_scalingInverseWithOneScaleDimensionZero_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:142:10: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
142 | scale(testVectors_);
| ~~~~~^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:143:35: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
143 | scale.inverseIgnoringZeroScale(testVectors_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 74%] Built target ewald-test
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrunutility-test-shared
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests/threadaffinitytest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gpu_utils-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gpu_utils-test.dir/gputest.cpp.o CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gpu_utils-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 74%] Built target gpu_utils-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/densityfit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/densityfit.cpp
/usr/bin/make -f src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build.make src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdspan-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests/accessor_policy.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/extents.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests/extents.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -P CMakeFiles/mdrunutility-test-shared.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test-shared.dir/link.txt --verbose=1
/usr/bin/ar qc ../../../../lib/libmdrunutility-test-shared.a CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o
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make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 74%] Built target mdrunutility-test-shared
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/dofit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/dofit.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/extensions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests/extensions.cpp
/usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/DependInfo.cmake --color=
Scanning dependencies of target onlinehelp-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/helpformat.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/textreader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/textreader.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/exponentialmovingaverage.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/layouts.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests/layouts.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/helpmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/mdspan.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests/mdspan.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/functions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/functions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/helpwritercontext.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/functions.cpp:49:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvcbrtInteger_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_SixthrootDouble_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_SixthrootInteger_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_ErfInvDouble_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsixthrootInteger_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
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/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsixthrootDouble_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
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/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsqrtDouble_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
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/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsqrtInteger_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
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/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvcbrtDouble_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
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/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/onlinehelp-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 75%] Built target onlinehelp-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/gausstransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/gausstransform.cpp
/usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/options/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/CMakeFiles/options-test.dir/DependInfo.cmake --color=
Scanning dependencies of target options-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/abstractoptionstorage.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/textwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/textwriter.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/typetraits.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/typetraits.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/utility-test.dir/alignedallocator.cpp.o CMakeFiles/utility-test.dir/arrayref.cpp.o CMakeFiles/utility-test.dir/bitmask32.cpp.o CMakeFiles/utility-test.dir/bitmask64.cpp.o CMakeFiles/utility-test.dir/bitmask128.cpp.o CMakeFiles/utility-test.dir/cstringutil.cpp.o CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o CMakeFiles/utility-test.dir/logger.cpp.o CMakeFiles/utility-test.dir/mutex.cpp.o CMakeFiles/utility-test.dir/path.cpp.o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o CMakeFiles/utility-test.dir/stringutil.cpp.o CMakeFiles/utility-test.dir/textreader.cpp.o CMakeFiles/utility-test.dir/textwriter.cpp.o CMakeFiles/utility-test.dir/typetraits.cpp.o CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/utility-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 76%] Built target utility-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/densityfittingforce.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/densityfittingforce.cpp
/usr/bin/make -f src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build.make src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/pbcutil/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pbcutil/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/DependInfo.cmake --color=
Scanning dependencies of target pbcutil-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pbcutil/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pbcutil-test.dir/pbc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/tests/pbc.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pbcutil/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/tests/pbcenums.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/invertmatrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/invertmatrix.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pbcutil/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pbcutil-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pbcutil-test.dir/pbc.cpp.o CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pbcutil-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 76%] Built target pbcutil-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/matrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/matrix.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/filenameoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/filenameoption.cpp
/usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/random/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/CMakeFiles/random-test.dir/DependInfo.cmake --color=
Scanning dependencies of target random-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/exponentialdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/exponentialdistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdspan-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o CMakeFiles/mdspan-test.dir/extents.cpp.o CMakeFiles/mdspan-test.dir/extensions.cpp.o CMakeFiles/mdspan-test.dir/layouts.cpp.o CMakeFiles/mdspan-test.dir/mdspan.cpp.o CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdspan-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 76%] Built target mdspan-test
/usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/restraint/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/restraint/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/DependInfo.cmake --color=
Scanning dependencies of target restraintpotential-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/restraint/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/restraint/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/restraintpotential-test.dir/manager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/restraint/tests/manager.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/exponentialdistribution.cpp:45:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ExponentialDistributionTest_Output_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/restraint/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/restraint/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/multidimarray.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/multidimarray.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/gammadistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/gammadistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/filenameoptionmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/restraint/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/restraintpotential-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/restraintpotential-test.dir/manager.cpp.o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/restraintpotential-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 76%] Built target restraintpotential-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/normaldistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/normaldistribution.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/gammadistribution.cpp:45:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::GammaDistributionTest_Output_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/normaldistribution.cpp:45:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::NormalDistributionTest_Output_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/tables/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tables/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tables/tests/CMakeFiles/table-test.dir/DependInfo.cmake --color=
Scanning dependencies of target table-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tables/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tables/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/table-test.dir/splinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/seed.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/seed.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/paddedvector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/tabulatednormaldistribution.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_NumericalInputPmeCorr_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::CubicSplineTable]':
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:515:15: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
515 | TypeParam pmeCorrTable({ { "NumericalPMECorr", functionValues, derivativeValues, inputSpacing } },
| ^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/option.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/option.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/tabulatednormaldistribution.cpp:45:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/optionsassigner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/optionsassigner.cpp
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::TabulatedNormalDistributionTest_OutputDouble14_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_NumericalInputPmeCorr_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::QuadraticSplineTable]':
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:515:15: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
515 | TypeParam pmeCorrTable({ { "NumericalPMECorr", functionValues, derivativeValues, inputSpacing } },
| ^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/threefry.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_HandlesIncorrectNumericalInput_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::QuadraticSplineTable]':
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:457:13: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
457 | TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.001 } }, { 1.0, 2.0 }),
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:189:5: note: in expansion of macro 'GMX_TEST_THROW_'
189 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:456:5: note: in expansion of macro 'EXPECT_THROW_GMX'
456 | EXPECT_THROW_GMX(
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:463:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
463 | EXPECT_THROW_GMX(TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.1 } }, { 1.0, 2.0 }),
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:189:5: note: in expansion of macro 'GMX_TEST_THROW_'
189 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:463:5: note: in expansion of macro 'EXPECT_THROW_GMX'
463 | EXPECT_THROW_GMX(TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.1 } }, { 1.0, 2.0 }),
| ^~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:485:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
485 | EXPECT_THROW_GMX(TypeParam({ { "NumericalBadLJ12", functionValues, badDerivativeValues, spacing } },
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:189:5: note: in expansion of macro 'GMX_TEST_THROW_'
189 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:485:5: note: in expansion of macro 'EXPECT_THROW_GMX'
485 | EXPECT_THROW_GMX(TypeParam({ { "NumericalBadLJ12", functionValues, badDerivativeValues, spacing } },
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:492:13: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
492 | TypeParam({ { "NumericalLJ12", functionValues, derivativeValues, spacing } }, { 0.2, 1.0 }),
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:189:5: note: in expansion of macro 'GMX_TEST_THROW_'
189 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:491:5: note: in expansion of macro 'EXPECT_THROW_GMX'
491 | EXPECT_THROW_GMX(
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_HandlesIncorrectNumericalInput_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::CubicSplineTable]':
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:457:13: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
457 | TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.001 } }, { 1.0, 2.0 }),
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:189:5: note: in expansion of macro 'GMX_TEST_THROW_'
189 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:456:5: note: in expansion of macro 'EXPECT_THROW_GMX'
456 | EXPECT_THROW_GMX(
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:463:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
463 | EXPECT_THROW_GMX(TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.1 } }, { 1.0, 2.0 }),
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:189:5: note: in expansion of macro 'GMX_TEST_THROW_'
189 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:463:5: note: in expansion of macro 'EXPECT_THROW_GMX'
463 | EXPECT_THROW_GMX(TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.1 } }, { 1.0, 2.0 }),
| ^~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:485:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
485 | EXPECT_THROW_GMX(TypeParam({ { "NumericalBadLJ12", functionValues, badDerivativeValues, spacing } },
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:189:5: note: in expansion of macro 'GMX_TEST_THROW_'
189 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:485:5: note: in expansion of macro 'EXPECT_THROW_GMX'
485 | EXPECT_THROW_GMX(TypeParam({ { "NumericalBadLJ12", functionValues, badDerivativeValues, spacing } },
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:492:13: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
492 | TypeParam({ { "NumericalLJ12", functionValues, derivativeValues, spacing } }, { 0.2, 1.0 }),
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:189:5: note: in expansion of macro 'GMX_TEST_THROW_'
189 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:491:5: note: in expansion of macro 'EXPECT_THROW_GMX'
491 | EXPECT_THROW_GMX(
| ^~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /usr/include/c++/9/bits/random.h:34,
from /usr/include/c++/9/random:49,
from /<<PKGBUILDDIR>>/src/gromacs/random/seed.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/random/threefry.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:43:
/usr/include/c++/9/bits/stl_vector.h: In constructor 'std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/9/bits/stl_vector.h:622:7: note: parameter passing for argument of type 'std::initializer_list<long long unsigned int>' changed in GCC 7.1
622 | vector(initializer_list<value_type> __l,
| ^~~~~~
In file included from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:59:
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::fillInputContents(gmx::ArrayRef<gmx::BasicVector<ValueType> >, int) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:69:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
69 | void fillInputContents(ArrayRef<BasicVector<T>> inputRef, int scaleFactor)
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp: In function 'void __static_initialization_and_destruction_0(int, int)':
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:117:54: note: parameter passing for argument of type 'std::initializer_list<long long unsigned int>' changed in GCC 7.1
117 | const std::vector<uint64_t> bitsZero{ { 0, 0, 0, 0 } };
| ^
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:127:87: note: parameter passing for argument of type 'std::initializer_list<long long unsigned int>' changed in GCC 7.1
127 | 0xFFFFFFFFFFFFFFFFULL, 0xFFFFFFFFFFFFFFFFULL } };
| ^
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:136:86: note: parameter passing for argument of type 'std::initializer_list<long long unsigned int>' changed in GCC 7.1
136 | 0xa4093822299f31d0ULL, 0x082efa98ec4e6c89ULL } };
| ^
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::compareViews(gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:94:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
94 | void compareViews(ArrayRef<T> input, ArrayRef<T> output)
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:94:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::compareViews(gmx::ArrayRef<gmx::BasicVector<ValueType> >, gmx::ArrayRef<gmx::BasicVector<ValueType> >) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:105:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
105 | void compareViews(ArrayRef<BasicVector<T>> input, ArrayRef<BasicVector<T>> output)
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:105:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/uniformintdistribution.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/9/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<double, std::allocator<double> >]':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<double, std::allocator<double> >]':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tables/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tables/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/9/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >]':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >]':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tables/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/table-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/table-test.dir/splinetable.cpp.o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/table-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 77%] Built target table-test
/usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/taskassignment/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/taskassignment/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/DependInfo.cmake --color=
Scanning dependencies of target taskassignment-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/taskassignment/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/taskassignment/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/tests/usergpuids.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/repeatingsection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/repeatingsection.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/9/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >]':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >]':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/uniformrealdistribution.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/9/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > >]':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > >]':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/uniformrealdistribution.cpp:45:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::UniformRealDistributionTest_GenerateCanonical_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::UniformRealDistributionTest_Output_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/vectypes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/vectypes.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/random-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/random-test.dir/exponentialdistribution.cpp.o CMakeFiles/random-test.dir/gammadistribution.cpp.o CMakeFiles/random-test.dir/normaldistribution.cpp.o CMakeFiles/random-test.dir/seed.cpp.o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o CMakeFiles/random-test.dir/threefry.cpp.o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/random-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 78%] Built target random-test
/usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/topology/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests/CMakeFiles/topology-test.dir/DependInfo.cmake --color=
Scanning dependencies of target topology-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/topology-test.dir/exclusionblocks.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/tests/exclusionblocks.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/taskassignment/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/taskassignment/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/timeunitmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/timeunitmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/taskassignment/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/taskassignment-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/taskassignment-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 78%] Built target taskassignment-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/topology-test.dir/mtop.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/tests/mtop.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/vectypes.cpp:50:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double (&)[3]}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/pulling/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pulling/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/DependInfo.cmake --color=
Scanning dependencies of target pull-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void {anonymous}::RVecTest_ConvertsImplicitlyFrom_rvec_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pulling/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pulling/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pull-test.dir/pull.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/tests/pull.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/topology-test.dir/symtab.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/tests/symtab.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pulling/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pulling/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/treesupport.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/treesupport.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/math-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o CMakeFiles/math-test.dir/coordinatetransformation.cpp.o CMakeFiles/math-test.dir/densityfit.cpp.o CMakeFiles/math-test.dir/dofit.cpp.o CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o CMakeFiles/math-test.dir/functions.cpp.o CMakeFiles/math-test.dir/gausstransform.cpp.o CMakeFiles/math-test.dir/densityfittingforce.cpp.o CMakeFiles/math-test.dir/invertmatrix.cpp.o CMakeFiles/math-test.dir/matrix.cpp.o CMakeFiles/math-test.dir/multidimarray.cpp.o CMakeFiles/math-test.dir/paddedvector.cpp.o CMakeFiles/math-test.dir/vectypes.cpp.o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/math-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pulling/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pull-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pull-test.dir/pull.cpp.o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pull-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 78%] Built target pull-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 80%] Built target math-test
/usr/bin/make -f src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/awh/tests/CMakeFiles/awh-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/awh/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/awh/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/awh/tests/CMakeFiles/awh-test.dir/DependInfo.cmake --color=
Scanning dependencies of target awh-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/awh-test.dir/bias.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/tests/bias.cpp
/usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/simd/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/CMakeFiles/simd-test.dir/DependInfo.cmake --color=
Scanning dependencies of target simd-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/bootstrap_loadstore.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/topology-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/topology-test.dir/exclusionblocks.cpp.o CMakeFiles/topology-test.dir/mtop.cpp.o CMakeFiles/topology-test.dir/symtab.cpp.o CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/topology-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 80%] Built target topology-test
/usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/compat/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests/CMakeFiles/compat-test.dir/DependInfo.cmake --color=
Scanning dependencies of target compat-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -Wno-unused-member-function -o CMakeFiles/compat-test.dir/optional.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/compat/tests/optional.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/base.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/base.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/bias.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/awh/tests/bias.cpp:37:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, double&, double&}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In function 'gmx::test::AwhTestParameters gmx::test::getAwhTestParameters(int, int)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/awh/bias.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/awh/tests/bias.cpp:37:
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual void gmx::test::BiasTest_ForcesBiasPmf_Test::TestBody()':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/bias.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/awh/tests/bias.cpp:37:
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_floatingpoint.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_floatingpoint_util.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/options-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o CMakeFiles/options-test.dir/filenameoption.cpp.o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o CMakeFiles/options-test.dir/option.cpp.o CMakeFiles/options-test.dir/optionsassigner.cpp.o CMakeFiles/options-test.dir/repeatingsection.cpp.o CMakeFiles/options-test.dir/timeunitmanager.cpp.o CMakeFiles/options-test.dir/treesupport.cpp.o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/options-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_vector_operations.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 81%] Built target options-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/compat-test.dir/pointers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/compat/tests/pointers.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/awh-test.dir/biasstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/tests/biasstate.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_math.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_math.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_memory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_memory.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/awh-test.dir/grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/tests/grid.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/awh/tests/biasstate.cpp:37:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double, double, double&}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In constructor 'gmx::test::BiasStateTest::BiasStateTest()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_integer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_integer.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/dimparams.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/awh/grid.h:60,
from /<<PKGBUILDDIR>>/src/gromacs/awh/tests/grid.cpp:37:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&, double, const double&}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void gmx::test::gridTest_neighborhood_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/compat-test.dir/string_view.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/compat/tests/string_view.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd4.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/awh-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4_floatingpoint.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/awh/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/awh-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/awh-test.dir/bias.cpp.o CMakeFiles/awh-test.dir/biasstate.cpp.o CMakeFiles/awh-test.dir/grid.cpp.o CMakeFiles/awh-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/awh-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 81%] Built target awh-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4_vector_operations.cpp
/usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/DependInfo.cmake --color=
Scanning dependencies of target gmxana-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxana-test.dir/entropy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/entropy.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/gmx_traj.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd4_math.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4_math.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/entropy.cpp:43:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/entropy.cpp:43:
/usr/include/c++/9/bits/stl_vector.h: In member function 'void gmx::{anonymous}::Entropy::runQuasiHarmonic(real, gmx_bool)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In function 'void gmx::{anonymous}::Entropy::runSchlitter(real, gmx_bool)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/DependInfo.cmake --color=
Scanning dependencies of target pdb2gmx3-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=1 -DCHARMM=1 -DGMX_DOUBLE=1 -DGROMOS=0 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/scalar.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/scalar.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/gmx_mindist.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxana-test.dir/gmx_msd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/gmx_msd.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/scalar_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/scalar_util.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxana-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gmxana-test.dir/entropy.cpp.o CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o CMakeFiles/gmxana-test.dir/gmx_msd.cpp.o CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gmxana-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 82%] Built target gmxana-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=1 -DCHARMM=1 -DGMX_DOUBLE=1 -DGROMOS=0 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/DependInfo.cmake --color=
Scanning dependencies of target pdb2gmx2-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=1 -DGROMOS=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx3-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pdb2gmx3-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/scalar_math.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/scalar_math.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 83%] Built target pdb2gmx3-test
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/DependInfo.cmake --color=
Scanning dependencies of target pdb2gmx1-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=1 -DGROMOS=0 -DHAVE_CONFIG_H -DOPLSAA=1 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/compat-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/compat-test.dir/optional.cpp.o CMakeFiles/compat-test.dir/pointers.cpp.o CMakeFiles/compat-test.dir/string_view.cpp.o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/compat-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 84%] Built target compat-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=1 -DGROMOS=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/DependInfo.cmake --color=
Scanning dependencies of target gmxpreprocess-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/editconf.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/simd-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o CMakeFiles/simd-test.dir/base.cpp.o CMakeFiles/simd-test.dir/simd.cpp.o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o CMakeFiles/simd-test.dir/simd_math.cpp.o CMakeFiles/simd-test.dir/simd_memory.cpp.o CMakeFiles/simd-test.dir/simd_integer.cpp.o CMakeFiles/simd-test.dir/simd4.cpp.o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o CMakeFiles/simd-test.dir/simd4_math.cpp.o CMakeFiles/simd-test.dir/scalar.cpp.o CMakeFiles/simd-test.dir/scalar_util.cpp.o CMakeFiles/simd-test.dir/scalar_math.cpp.o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/simd-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 85%] Built target simd-test
/usr/bin/make -f src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build.make src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/DependInfo.cmake --color=
Scanning dependencies of target correlations-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build.make src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/correlations-test.dir/autocorr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/autocorr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/genconf.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx2-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pdb2gmx2-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/autocorr.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/autocorr.cpp:45:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacRcross_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 85%] Built target pdb2gmx2-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/manyautocorrelation.cpp
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacP3_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacNormal_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacP4_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacP2_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacP0_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/genion.cpp
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacP1_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacNoNormalize_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacCos_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacVector_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=1 -DGROMOS=0 -DHAVE_CONFIG_H -DOPLSAA=1 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/DependInfo.cmake --color=
Scanning dependencies of target analysisdata-test-shared
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/datatest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/correlations-test.dir/correlationdataset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/correlationdataset.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx1-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pdb2gmx1-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/genrestr.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 85%] Built target pdb2gmx1-test
/usr/bin/make -f src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build.make src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/DependInfo.cmake --color=
Scanning dependencies of target coordinateio-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build.make src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/builder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/builder.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/correlations-test.dir/expfit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/expfit.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/datatest.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/datatest.cpp:44:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&}; _Tp = gmx::test::AnalysisDataTestInputPointSet::Value; _Alloc = std::allocator<gmx::test::AnalysisDataTestInputPointSet::Value>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::test::AnalysisDataTestInputPointSet::Value>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, double&}; _Tp = gmx::test::AnalysisDataTestInputPointSet::Value; _Alloc = std::allocator<gmx::test::AnalysisDataTestInputPointSet::Value>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::test::AnalysisDataTestInputPointSet::Value>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >'} changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In member function 'void gmx::test::AnalysisDataTestInputFrame::addPointSetWithValues(int, int, real)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void gmx::test::AnalysisDataTestInputFrame::addPointSetWithValueAndError(int, int, real, real)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp
/usr/include/c++/9/bits/vector.tcc: In member function 'void gmx::test::AnalysisDataTestInput::addFrameWithValueAndError(real, real, real)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void gmx::test::AnalysisDataTestInput::addFrameWithValues(real, real, real)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void gmx::test::AnalysisDataTestInput::addFrameWithValues(real, real, real, real)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void gmx::test::AnalysisDataTestInput::addFrameWithValues(real, real)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void gmx::test::AnalysisDataTestInputFrame::addPointSetWithValues(int, int, real, real)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void gmx::test::AnalysisDataTestInputFrame::addPointSetWithValues(int, int, real, real, real)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/mock_datamodule.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/expfit.cpp:51:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In static member function 'static void gmx::{anonymous}::ExpfitTest::SetUpTestCase()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::PreprocessingAtomTypesTest_CorrectNameFound_Test]':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
61 | PreprocessingAtomTypesTest() : nb_({}, {}) { open_symtab(&symtab_); }
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::PreprocessingAtomTypesTest_NoNameFromIncorrectTypeNumber_Test]':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
61 | PreprocessingAtomTypesTest() : nb_({}, {}) { open_symtab(&symtab_); }
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::PreprocessingAtomTypesTest_CorrectNameFromTypeNumber_Test]':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
61 | PreprocessingAtomTypesTest() : nb_({}, {}) { open_symtab(&symtab_); }
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::PreprocessingAtomTypesTest_WrongNameNotFound_Test]':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
61 | PreprocessingAtomTypesTest() : nb_({}, {}) { open_symtab(&symtab_); }
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::PreprocessingAtomTypesTest_EmptyOnCreate_Test]':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
61 | PreprocessingAtomTypesTest() : nb_({}, {}) { open_symtab(&symtab_); }
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::PreprocessingAtomTypesTest_AddTypeWorks_Test]':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
61 | PreprocessingAtomTypesTest() : nb_({}, {}) { open_symtab(&symtab_); }
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::PreprocessingAtomTypesTest_CannotAddDuplicateEntry_Test]':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
61 | PreprocessingAtomTypesTest() : nb_({}, {}) { open_symtab(&symtab_); }
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::PreprocessingAtomTypesTest_AddMultipleTypesWorks_Test]':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
61 | PreprocessingAtomTypesTest() : nb_({}, {}) { open_symtab(&symtab_); }
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::PreprocessingAtomTypesTest_IndexOutOfRangeInvalid_Test]':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
61 | PreprocessingAtomTypesTest() : nb_({}, {}) { open_symtab(&symtab_); }
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/correlations-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/correlations-test.dir/autocorr.cpp.o CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o CMakeFiles/correlations-test.dir/correlationdataset.cpp.o CMakeFiles/correlations-test.dir/expfit.cpp.o CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/correlations-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 86%] Built target correlations-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_bond_atomtype.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/insert_molecules.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/outputadaptercontainer.cpp
/usr/bin/make -f src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build.make src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/energyanalysis/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/DependInfo.cmake --color=
Scanning dependencies of target energyanalysis-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build.make src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/energyanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/legacyenergy.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/outputadapters.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/readir.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/energyanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/energyanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/energyanalysis-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/energyanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 86%] Built target energyanalysis-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/requirements.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/requirements.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/solvate.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/topdirs.cpp
/usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/tools/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/CMakeFiles/tool-test.dir/DependInfo.cmake --color=
Scanning dependencies of target tool-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/tool-test.dir/dump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/tests/dump.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/cmake -P CMakeFiles/analysisdata-test-shared.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test-shared.dir/link.txt --verbose=1
/usr/bin/ar qc ../../../../lib/libanalysisdata-test-shared.a CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o
/usr/bin/ranlib ../../../../lib/libanalysisdata-test-shared.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 86%] Built target analysisdata-test-shared
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/setatoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/setatoms.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/tool-test.dir/report_methods.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/tests/report_methods.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxpreprocess-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gmxpreprocess-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 87%] Built target gmxpreprocess-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/tool-test.dir/trjconv.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/tests/trjconv.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/setbothtime.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/setstarttime.cpp
/usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/fileio/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/DependInfo.cmake --color=
Scanning dependencies of target fileio-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/confio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/confio.cpp
/usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/selection/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests/CMakeFiles/selection-test.dir/DependInfo.cmake --color=
Scanning dependencies of target selection-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/indexutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/indexutil.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/settimestep.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/settimestep.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/tool-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/tool-test.dir/dump.cpp.o CMakeFiles/tool-test.dir/report_methods.cpp.o CMakeFiles/tool-test.dir/trjconv.cpp.o CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/tool-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 88%] Built target tool-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/testmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/testmodule.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/confio.cpp:48:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {int, int, int}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'testing::Test* testing::internal::ParameterizedTestFactory<TestClass>::CreateTest() [with TestClass = {anonymous}::StructureIORoundtripTest_ReadWriteTpsConf_Test]':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/nbsearch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/coordinateio-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/coordinateio-test.dir/builder.cpp.o CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o CMakeFiles/coordinateio-test.dir/requirements.cpp.o CMakeFiles/coordinateio-test.dir/setatoms.cpp.o CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o CMakeFiles/coordinateio-test.dir/settimestep.cpp.o CMakeFiles/coordinateio-test.dir/testmodule.cpp.o CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/coordinateio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 88%] Built target coordinateio-test
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/depend
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/filemd5.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/filemd5.cpp
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-mpi-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/domain_decomposition.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:49:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const {anonymous}::NeighborhoodSearchTestData::RefPair&}; _Tp = {anonymous}::NeighborhoodSearchTestData::RefPair; _Alloc = std::allocator<{anonymous}::NeighborhoodSearchTestData::RefPair>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair>::iterator' {aka '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:49:
/usr/include/c++/9/bits/stl_vector.h: In function 'void {anonymous}::NeighborhoodSearchTestData::computeReferencesInternal(t_pbc*, bool)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/minimize.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/minimize.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/mrcserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcserializer.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:49:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double (&)[3]}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In function 'void {anonymous}::NeighborhoodSearchTest::testPairSearch(gmx::AnalysisNeighborhoodSearch*, const {anonymous}::NeighborhoodSearchTestData&)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::BasicVector<double>}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/poscalc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/poscalc.cpp
/usr/include/c++/9/bits/vector.tcc: In function 'void {anonymous}::NeighborhoodSearchTest::testPairSearchIndexed(gmx::AnalysisNeighborhood*, const {anonymous}::NeighborhoodSearchTestData&, uint64_t)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_SimpleSelfPairsSearch_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:49:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:49:
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In function 'void {anonymous}::NeighborhoodSearchTestData::generateRandomRefPositions(int)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:49:
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_SimpleSearchExclusions_Test::TestBody()':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:49:
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:49:
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_GridSelfPairsSearch_Test::TestBody()':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:49:
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:49:
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_GridSearchTriclinic_Test::TestBody()':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_GridSearch2DPBC_Test::TestBody()':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_SimpleSearch_Test::TestBody()':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_GridSearchBox_Test::TestBody()':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_GridSearchExclusions_Test::TestBody()':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:49:
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_HandlesConcurrentSearches_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:49:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:49:
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymap.cpp
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_HandlesNoPBC_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_HandlesSkippingPairs_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:49:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:49:
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_HandlesNullPBC_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In function '{anonymous}::RandomBoxXYFullPBCData::RandomBoxXYFullPBCData()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:49:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/selectioncollection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/selectioncollection.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/selectionoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/selectionoption.cpp
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymap.cpp: In member function 'virtual void gmx::test::{anonymous}::MrcDensityMap_ReadsCoordinateTransformationFromFile_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymap.cpp:110:29: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
110 | coordinateTransformation({ &coordinate1, &coordinate1 + 1 });
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymap.cpp:111:29: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
111 | coordinateTransformation({ &coordinate2, &coordinate2 + 1 });
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymapheader.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/mimic.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/multisim.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/multisim.cpp
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymapheader.cpp: In member function 'virtual void gmx::MrcDensityMapHeaderTest_GetsCorrectCoordinateTransformNoOriginGiven_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymapheader.cpp:87:49: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
87 | getCoordinateTransformationToLattice(header)(testVectors);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymapheader.cpp: In member function 'virtual void gmx::MrcDensityMapHeaderTest_GetsCorrectCoordinateTransformWithOriginDefined_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymapheader.cpp:106:49: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
106 | getCoordinateTransformationToLattice(header)(testVectors);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymapheader.cpp: In member function 'virtual void gmx::MrcDensityMapHeaderTest_GetsCorrectCoordinateTransformWithStartValues_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymapheader.cpp:124:49: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
124 | getCoordinateTransformationToLattice(header)(testVectors);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/readinp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/readinp.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/multisimtest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/multisimtest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/fileioxdrserializer.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/pmetest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/pmetest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/tngio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/tngio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileio-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/fileio-test.dir/confio.cpp.o CMakeFiles/fileio-test.dir/filemd5.cpp.o CMakeFiles/fileio-test.dir/mrcserializer.cpp.o CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o CMakeFiles/fileio-test.dir/readinp.cpp.o CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o CMakeFiles/fileio-test.dir/tngio.cpp.o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/fileio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 89%] Built target fileio-test
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/compressed_x_output.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/compressed_x_output.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/replicaexchange.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/replicaexchange.cpp
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/depend
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cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-non-integrator-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-non-integrator-test.dir/minimize.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/minimize.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/densityfittingmodule.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/densityfittingmodule.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/toputils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/toputils.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o CMakeFiles/mdrun-mpi-test.dir/minimize.cpp.o CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o CMakeFiles/mdrun-mpi-test.dir/multisim.cpp.o CMakeFiles/mdrun-mpi-test.dir/multisimtest.cpp.o CMakeFiles/mdrun-mpi-test.dir/pmetest.cpp.o CMakeFiles/mdrun-mpi-test.dir/replicaexchange.cpp.o CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 89%] Built target mdrun-mpi-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/nonbonded_bench.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/selection-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/selection-test.dir/indexutil.cpp.o CMakeFiles/selection-test.dir/nbsearch.cpp.o CMakeFiles/selection-test.dir/poscalc.cpp.o CMakeFiles/selection-test.dir/selectioncollection.cpp.o CMakeFiles/selection-test.dir/selectionoption.cpp.o CMakeFiles/selection-test.dir/toputils.cpp.o CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/selection-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/exactcontinuation.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/exactcontinuation.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 90%] Built target selection-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/normalmodes.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/grompp.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/grompp.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/rerun.cpp
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-tpi-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/tpitest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-tpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-tpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/helpwriting.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/helpwriting.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 91%] Built target mdrun-tpi-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/initialconstraints.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/initialconstraints.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/simple_mdrun.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/interactiveMD.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/interactiveMD.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/outputfiles.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/outputfiles.cpp
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-mpi-coordination-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-coordination-test.dir/periodicactions.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/periodicactions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-coordination-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/orires.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/orires.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-non-integrator-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-non-integrator-test.dir/minimize.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-non-integrator-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
/usr/bin/make -f src/api/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/build.make src/api/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/api/cpp/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/DependInfo.cmake --color=
Scanning dependencies of target gmxapi-mpi-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/restraint.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/restraint.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 92%] Built target mdrun-non-integrator-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/pmetest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/pmetest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/status.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/status.cpp
/usr/bin/make -f src/api/cpp/tests/CMakeFiles/gmxapi-test.dir/build.make src/api/cpp/tests/CMakeFiles/gmxapi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/api/cpp/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/CMakeFiles/gmxapi-test.dir/DependInfo.cmake --color=
Scanning dependencies of target gmxapi-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/api/cpp/tests/CMakeFiles/gmxapi-test.dir/build.make src/api/cpp/tests/CMakeFiles/gmxapi-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/restraint.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/restraint.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/system.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/system.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/simulator.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/simulator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/version.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/version.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/status.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/status.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-coordination-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-mpi-coordination-test.dir/periodicactions.cpp.o CMakeFiles/mdrun-mpi-coordination-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-coordination-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 93%] Built target mdrun-mpi-coordination-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/api/cpp/workflow/tests/CMakeFiles/workflow-details-mpi-test.dir/build.make src/api/cpp/workflow/tests/CMakeFiles/workflow-details-mpi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/api/cpp/workflow/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests/CMakeFiles/workflow-details-mpi-test.dir/DependInfo.cmake --color=
Scanning dependencies of target workflow-details-mpi-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/api/cpp/workflow/tests/CMakeFiles/workflow-details-mpi-test.dir/build.make src/api/cpp/workflow/tests/CMakeFiles/workflow-details-mpi-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/workflow-details-mpi-test.dir/workflow.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/workflow/tests/workflow.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/system.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/system.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/runner.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/runner.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/version.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/version.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/workflow-details-mpi-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/stopsignaler.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/stopsignaler.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/workflow-details-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/workflow-details-mpi-test.dir/workflow.cpp.o CMakeFiles/workflow-details-mpi-test.dir/__/__/__/__/testutils/unittest_main.cpp.o ../../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../../bin/workflow-details-mpi-test ../../../../../lib/libtestutils.a ../../../../../lib/libgmxapi_d.so.0.1.0 ../../../../../lib/libmdrun_test_infrastructure.a ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../../lib/libgmock.so ../../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/runner.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/runner.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 93%] Built target workflow-details-mpi-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/swapcoords.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/swapcoords.cpp
/usr/bin/make -f src/api/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build.make src/api/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/api/cpp/workflow/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/DependInfo.cmake --color=
Scanning dependencies of target workflow-details-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/api/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build.make src/api/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/workflow-details-test.dir/workflow.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/workflow/tests/workflow.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/tabulated_bonded_interactions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/stopsignaler.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/termination.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/termination.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gmxapi-mpi-test.dir/restraint.cpp.o CMakeFiles/gmxapi-mpi-test.dir/status.cpp.o CMakeFiles/gmxapi-mpi-test.dir/system.cpp.o CMakeFiles/gmxapi-mpi-test.dir/version.cpp.o CMakeFiles/gmxapi-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/gmxapi-mpi-test.dir/runner.cpp.o CMakeFiles/gmxapi-mpi-test.dir/stopsignaler.cpp.o ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/gmxapi-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgmxapi_d.so.0.1.0 ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 93%] Built target gmxapi-mpi-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/trajectory_writing.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/trajectory_writing.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/workflow-details-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/workflow-details-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/workflow-details-test.dir/workflow.cpp.o CMakeFiles/workflow-details-test.dir/__/__/__/__/testutils/unittest_main.cpp.o ../../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../../bin/workflow-details-test ../../../../../lib/libtestutils.a ../../../../../lib/libgmxapi_d.so.0.1.0 ../../../../../lib/libmdrun_test_infrastructure.a ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../../lib/libgmock.so ../../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 94%] Built target workflow-details-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/mimic.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/mimic.cpp
/usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/commandline/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/DependInfo.cmake --color=
Scanning dependencies of target commandline-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinehelpmodule.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gmxapi-test.dir/restraint.cpp.o CMakeFiles/gmxapi-test.dir/status.cpp.o CMakeFiles/gmxapi-test.dir/system.cpp.o CMakeFiles/gmxapi-test.dir/version.cpp.o CMakeFiles/gmxapi-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/gmxapi-test.dir/runner.cpp.o CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/gmxapi-test ../../../../lib/libtestutils.a ../../../../lib/libgmxapi_d.so.0.1.0 ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 95%] Built target gmxapi-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrunutility-mpi-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests/threadaffinity_mpi.cpp
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrunutility-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests/threadaffinity.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-test.dir/compressed_x_output.cpp.o CMakeFiles/mdrun-test.dir/densityfittingmodule.cpp.o CMakeFiles/mdrun-test.dir/exactcontinuation.cpp.o CMakeFiles/mdrun-test.dir/grompp.cpp.o CMakeFiles/mdrun-test.dir/helpwriting.cpp.o CMakeFiles/mdrun-test.dir/initialconstraints.cpp.o CMakeFiles/mdrun-test.dir/interactiveMD.cpp.o CMakeFiles/mdrun-test.dir/outputfiles.cpp.o CMakeFiles/mdrun-test.dir/orires.cpp.o CMakeFiles/mdrun-test.dir/pmetest.cpp.o CMakeFiles/mdrun-test.dir/simulator.cpp.o CMakeFiles/mdrun-test.dir/swapcoords.cpp.o CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o CMakeFiles/mdrun-test.dir/termination.cpp.o CMakeFiles/mdrun-test.dir/trajectory_writing.cpp.o CMakeFiles/mdrun-test.dir/mimic.cpp.o CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 96%] Built target mdrun-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinehelpwriter.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdrunutility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
/usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/DependInfo.cmake --color=
Scanning dependencies of target analysisdata-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/analysisdata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinemodulemanager.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 97%] Built target mdrunutility-mpi-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinemodulemanagertest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdrunutility-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 97%] Built target mdrunutility-test
/usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/DependInfo.cmake --color=
Scanning dependencies of target trajectoryanalysis-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/moduletest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/cmdlinerunner.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlineparser.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlineprogramcontext.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/filenm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/filenm.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/pargs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/pargs.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/analysisdata-test.dir/arraydata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/arraydata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/angle.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/convert_trj.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/distance.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/analysisdata-test.dir/average.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/average.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/analysisdata-test.dir/histogram.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/histogram.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/extract_cluster.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/commandline-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o CMakeFiles/commandline-test.dir/filenm.cpp.o CMakeFiles/commandline-test.dir/pargs.cpp.o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/commandline-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 98%] Built target commandline-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/pairdist.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/rdf.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/sasa.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/select.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/topologyinformation.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/trajectory.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/unionfind.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, double&, double&}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/analysisdata-test.dir/lifetime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/lifetime.cpp
/usr/include/c++/9/bits/vector.tcc: In function 'void {anonymous}::SurfaceAreaTest::generateRandomPositions(int)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44:
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void {anonymous}::SurfaceAreaTest_ComputesSinglePoint_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44:
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void {anonymous}::SurfaceAreaTest_ComputesTwoPoints_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44:
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44:
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void {anonymous}::SurfaceAreaTest_ComputesTwoPointsOfUnequalRadius_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44:
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44:
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void {anonymous}::SurfaceAreaTest_SurfacePoints12_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44:
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void {anonymous}::SurfaceAreaTest_SurfacePoints32_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44:
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void {anonymous}::SurfaceAreaTest_SurfacePoints42_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44:
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void {anonymous}::SurfaceAreaTest_SurfacePoints122_Test::TestBody()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o CMakeFiles/analysisdata-test.dir/arraydata.cpp.o CMakeFiles/analysisdata-test.dir/average.cpp.o CMakeFiles/analysisdata-test.dir/histogram.cpp.o CMakeFiles/analysisdata-test.dir/lifetime.cpp.o CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/analysisdata-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 98%] Built target analysisdata-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/trajectoryanalysis-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/trajectoryanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[100%] Built target trajectoryanalysis-test
/usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/CMakeFiles/tests.dir/DependInfo.cmake --color=
Scanning dependencies of target tests
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
make[4]: Nothing to be done for 'CMakeFiles/tests.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[100%] Built target tests
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/build/basic-dp/CMakeFiles 0
make[2]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
make[1]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
(cd build/basic-dp; LD_LIBRARY_PATH=/<<PKGBUILDDIR>>/build/basic-dp/lib ctest -V || dpkg-architecture -i hurd-i386 )
UpdateCTestConfiguration from :/<<PKGBUILDDIR>>/build/basic-dp/DartConfiguration.tcl
Parse Config file:/<<PKGBUILDDIR>>/build/basic-dp/DartConfiguration.tcl
UpdateCTestConfiguration from :/<<PKGBUILDDIR>>/build/basic-dp/DartConfiguration.tcl
Parse Config file:/<<PKGBUILDDIR>>/build/basic-dp/DartConfiguration.tcl
Test project /<<PKGBUILDDIR>>/build/basic-dp
Constructing a list of tests
Done constructing a list of tests
Updating test list for fixtures
Added 0 tests to meet fixture requirements
Checking test dependency graph...
Checking test dependency graph end
test 1
Start 1: TestUtilsUnitTests
1: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/testutils-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/TestUtilsUnitTests.xml"
1: Test timeout computed to be: 30
1: [==========] Running 59 tests from 5 test cases.
1: [----------] Global test environment set-up.
1: [----------] 10 tests from InteractiveTestHelperTest
1: [ RUN ] InteractiveTestHelperTest.ChecksSimpleSession
1: [ OK ] InteractiveTestHelperTest.ChecksSimpleSession (4 ms)
1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline
1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline (2 ms)
1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput
1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput (1 ms)
1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput
1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput (2 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsIncorrectOutput
1: [ OK ] InteractiveTestHelperTest.DetectsIncorrectOutput (2 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsMissingOutput
1: [ OK ] InteractiveTestHelperTest.DetectsMissingOutput (6 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsMissingFinalOutput
1: [ OK ] InteractiveTestHelperTest.DetectsMissingFinalOutput (2 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsExtraOutput
1: [ OK ] InteractiveTestHelperTest.DetectsExtraOutput (2 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsMissingInput
1: [ OK ] InteractiveTestHelperTest.DetectsMissingInput (2 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsExtraInput
1: [ OK ] InteractiveTestHelperTest.DetectsExtraInput (1 ms)
1: [----------] 10 tests from InteractiveTestHelperTest (24 ms total)
1:
1: [----------] 34 tests from ReferenceDataTest
1: [ RUN ] ReferenceDataTest.HandlesSimpleData
1: [ OK ] ReferenceDataTest.HandlesSimpleData (0 ms)
1: [ RUN ] ReferenceDataTest.HandlesFloatingPointData
1: [ OK ] ReferenceDataTest.HandlesFloatingPointData (0 ms)
1: [ RUN ] ReferenceDataTest.HandlesPresenceChecks
1: [ OK ] ReferenceDataTest.HandlesPresenceChecks (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesStringBlockData
1: [ OK ] ReferenceDataTest.HandlesStringBlockData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesVectorData
1: [ OK ] ReferenceDataTest.HandlesVectorData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesSequenceData
1: [ OK ] ReferenceDataTest.HandlesSequenceData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesSequenceOfCustomData
1: [ OK ] ReferenceDataTest.HandlesSequenceOfCustomData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesIncorrectData
1: [ OK ] ReferenceDataTest.HandlesIncorrectData (2 ms)
1: [ RUN ] ReferenceDataTest.HandlesIncorrectDataType
1: [ OK ] ReferenceDataTest.HandlesIncorrectDataType (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesMissingData
1: [ OK ] ReferenceDataTest.HandlesMissingData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesUncheckedData
1: [ OK ] ReferenceDataTest.HandlesUncheckedData (0 ms)
1: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInSequence
1: [ OK ] ReferenceDataTest.HandlesUncheckedDataInSequence (2 ms)
1: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInCompound
1: [ OK ] ReferenceDataTest.HandlesUncheckedDataInCompound (0 ms)
1: [ RUN ] ReferenceDataTest.HandlesAnys
1: [ OK ] ReferenceDataTest.HandlesAnys (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesKeyValueTree
1: [ OK ] ReferenceDataTest.HandlesKeyValueTree (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeExtraKey
1: [ OK ] ReferenceDataTest.HandlesKeyValueTreeExtraKey (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeMissingKey
1: [ OK ] ReferenceDataTest.HandlesKeyValueTreeMissingKey (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectValue
1: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectValue (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectType
1: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectType (2 ms)
1: [ RUN ] ReferenceDataTest.HandlesMissingReferenceDataFile
1: [ OK ] ReferenceDataTest.HandlesMissingReferenceDataFile (0 ms)
1: [ RUN ] ReferenceDataTest.HandlesSpecialCharactersInStrings
1: [ OK ] ReferenceDataTest.HandlesSpecialCharactersInStrings (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace
1: [ OK ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesEmptyStrings
1: [ OK ] ReferenceDataTest.HandlesEmptyStrings (2 ms)
1: [ RUN ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock
1: [ OK ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesSequenceItemIndices
1: [ OK ] ReferenceDataTest.HandlesSequenceItemIndices (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData
1: [ OK ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesMultipleNullIds
1: [ OK ] ReferenceDataTest.HandlesMultipleNullIds (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds
1: [ OK ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds (2 ms)
1: [ RUN ] ReferenceDataTest.HandlesReadingValues
1: [ OK ] ReferenceDataTest.HandlesReadingValues (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges
1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges
1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges (2 ms)
1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges
1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges
1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges (2 ms)
1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries
1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries (1 ms)
1: [----------] 34 tests from ReferenceDataTest (42 ms total)
1:
1: [----------] 7 tests from FloatingPointDifferenceTest
1: [ RUN ] FloatingPointDifferenceTest.HandlesEqualValues
1: [ OK ] FloatingPointDifferenceTest.HandlesEqualValues (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesFloatValues
1: [ OK ] FloatingPointDifferenceTest.HandlesFloatValues (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign
1: [ OK ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero
1: [ OK ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferences
1: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferences (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero
1: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesNaN
1: [ OK ] FloatingPointDifferenceTest.HandlesNaN (0 ms)
1: [----------] 7 tests from FloatingPointDifferenceTest (0 ms total)
1:
1: [----------] 4 tests from FloatingPointToleranceTest
1: [ RUN ] FloatingPointToleranceTest.UlpTolerance
1: [ OK ] FloatingPointToleranceTest.UlpTolerance (0 ms)
1: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint
1: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint (0 ms)
1: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsUlp
1: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsUlp (0 ms)
1: [ RUN ] FloatingPointToleranceTest.DefaultFloatTolerance
1: [ OK ] FloatingPointToleranceTest.DefaultFloatTolerance (0 ms)
1: [----------] 4 tests from FloatingPointToleranceTest (0 ms total)
1:
1: [----------] 4 tests from XvgTests
1: [ RUN ] XvgTests.CreateFile
1: [ OK ] XvgTests.CreateFile (2 ms)
1: [ RUN ] XvgTests.CheckMissing
1: [ OK ] XvgTests.CheckMissing (2 ms)
1: [ RUN ] XvgTests.CheckExtra
1: [ OK ] XvgTests.CheckExtra (2 ms)
1: [ RUN ] XvgTests.ReadIncorrect
1: [ OK ] XvgTests.ReadIncorrect (2 ms)
1: [----------] 4 tests from XvgTests (9 ms total)
1:
1: [----------] Global test environment tear-down
1: [==========] 59 tests from 5 test cases ran. (75 ms total)
1: [ PASSED ] 59 tests.
1/52 Test #1: TestUtilsUnitTests .................. Passed 0.61 sec
test 2
Start 2: TestUtilsMpiUnitTests
2: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/testutils-mpi-test "-ntmpi" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/TestUtilsMpiUnitTests.xml"
2: Test timeout computed to be: 30
2: [==========] Running 1 test from 1 test case.
2: [----------] Global test environment set-up.
2: [----------] 1 test from MpiSelfTest
2: [ RUN ] MpiSelfTest.Runs
2: [ OK ] MpiSelfTest.Runs (2 ms)
2: [----------] 1 test from MpiSelfTest (2 ms total)
2:
2: [----------] Global test environment tear-down
2: [==========] 1 test from 1 test case ran. (2 ms total)
2: [ PASSED ] 1 test.
2/52 Test #2: TestUtilsMpiUnitTests ............... Passed 0.06 sec
test 3
Start 3: UtilityUnitTests
3: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/utility-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/UtilityUnitTests.xml"
3: Test timeout computed to be: 30
3: [==========] Running 347 tests from 56 test cases.
3: [----------] Global test environment set-up.
3: [----------] 5 tests from AllocatorTest/0, where TypeParam = gmx::Allocator<double, gmx::AlignedAllocationPolicy>
3: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment
3: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment
3: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (1 ms)
3: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment
3: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/0.Move
3: [ OK ] AllocatorTest/0.Move (0 ms)
3: [ RUN ] AllocatorTest/0.StatelessAllocatorUsesNoMemory
3: [ OK ] AllocatorTest/0.StatelessAllocatorUsesNoMemory (0 ms)
3: [----------] 5 tests from AllocatorTest/0 (1 ms total)
3:
3: [----------] 5 tests from AllocatorTest/1, where TypeParam = gmx::Allocator<double, gmx::PageAlignedAllocationPolicy>
3: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment
3: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment
3: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment
3: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (1 ms)
3: [ RUN ] AllocatorTest/1.Move
3: [ OK ] AllocatorTest/1.Move (0 ms)
3: [ RUN ] AllocatorTest/1.StatelessAllocatorUsesNoMemory
3: [ OK ] AllocatorTest/1.StatelessAllocatorUsesNoMemory (0 ms)
3: [----------] 5 tests from AllocatorTest/1 (1 ms total)
3:
3: [----------] 5 tests from AllocatorTest/2, where TypeParam = gmx::Allocator<int, gmx::AlignedAllocationPolicy>
3: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment
3: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment
3: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment
3: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/2.Move
3: [ OK ] AllocatorTest/2.Move (0 ms)
3: [ RUN ] AllocatorTest/2.StatelessAllocatorUsesNoMemory
3: [ OK ] AllocatorTest/2.StatelessAllocatorUsesNoMemory (0 ms)
3: [----------] 5 tests from AllocatorTest/2 (0 ms total)
3:
3: [----------] 5 tests from AllocatorTest/3, where TypeParam = gmx::Allocator<int, gmx::PageAlignedAllocationPolicy>
3: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment
3: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment
3: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (1 ms)
3: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment
3: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/3.Move
3: [ OK ] AllocatorTest/3.Move (0 ms)
3: [ RUN ] AllocatorTest/3.StatelessAllocatorUsesNoMemory
3: [ OK ] AllocatorTest/3.StatelessAllocatorUsesNoMemory (0 ms)
3: [----------] 5 tests from AllocatorTest/3 (1 ms total)
3:
3: [----------] 5 tests from AllocatorTest/4, where TypeParam = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>
3: [ RUN ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment
3: [ OK ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment
3: [ OK ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment (1 ms)
3: [ RUN ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment
3: [ OK ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment (1 ms)
3: [ RUN ] AllocatorTest/4.Move
3: [ OK ] AllocatorTest/4.Move (0 ms)
3: [ RUN ] AllocatorTest/4.StatelessAllocatorUsesNoMemory
3: [ OK ] AllocatorTest/4.StatelessAllocatorUsesNoMemory (0 ms)
3: [----------] 5 tests from AllocatorTest/4 (2 ms total)
3:
3: [----------] 5 tests from AllocatorTest/5, where TypeParam = gmx::Allocator<gmx::BasicVector<double>, gmx::PageAlignedAllocationPolicy>
3: [ RUN ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment
3: [ OK ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment
3: [ OK ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment (1 ms)
3: [ RUN ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment
3: [ OK ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/5.Move
3: [ OK ] AllocatorTest/5.Move (0 ms)
3: [ RUN ] AllocatorTest/5.StatelessAllocatorUsesNoMemory
3: [ OK ] AllocatorTest/5.StatelessAllocatorUsesNoMemory (0 ms)
3: [----------] 5 tests from AllocatorTest/5 (1 ms total)
3:
3: [----------] 1 test from AllocatorUntypedTest
3: [ RUN ] AllocatorUntypedTest.Comparison
3: [ OK ] AllocatorUntypedTest.Comparison (0 ms)
3: [----------] 1 test from AllocatorUntypedTest (0 ms total)
3:
3: [----------] 1 test from EmptyArrayRefTest
3: [ RUN ] EmptyArrayRefTest.IsEmpty
3: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms)
3: [----------] 1 test from EmptyArrayRefTest (1 ms total)
3:
3: [----------] 1 test from EmptyConstArrayRefTest
3: [ RUN ] EmptyConstArrayRefTest.IsEmpty
3: [ OK ] EmptyConstArrayRefTest.IsEmpty (0 ms)
3: [----------] 1 test from EmptyConstArrayRefTest (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef<char>
3: [ RUN ] ArrayRefTest/0.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/0.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/0.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/0.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/0.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/0.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/0.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/0.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/0 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef<unsigned char>
3: [ RUN ] ArrayRefTest/1.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/1.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/1.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/1.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/1.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/1.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/1.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/1.ConstructFromNonConstVectorWorks (1 ms)
3: [ RUN ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/1 (1 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef<int>
3: [ RUN ] ArrayRefTest/2.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/2.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/2.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/2.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/2.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/2.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/2.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/2.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/2 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef<unsigned int>
3: [ RUN ] ArrayRefTest/3.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/3.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/3.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/3.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/3.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/3.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/3.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/3.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/3 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/4, where TypeParam = gmx::ArrayRef<long>
3: [ RUN ] ArrayRefTest/4.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/4.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/4.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/4.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/4.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/4.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/4.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/4.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/4.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/4.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/4 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/5, where TypeParam = gmx::ArrayRef<unsigned long>
3: [ RUN ] ArrayRefTest/5.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/5.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/5.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/5.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/5.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/5.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/5.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/5.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/5.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/5.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/5 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/6, where TypeParam = gmx::ArrayRef<long long>
3: [ RUN ] ArrayRefTest/6.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/6.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/6.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/6.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/6.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/6.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/6.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/6.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/6.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/6.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/6 (1 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/7, where TypeParam = gmx::ArrayRef<unsigned long long>
3: [ RUN ] ArrayRefTest/7.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/7.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/7.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/7.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/7.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/7.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/7.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/7.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/7.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/7.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/7 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/8, where TypeParam = gmx::ArrayRef<float>
3: [ RUN ] ArrayRefTest/8.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/8.MakeWithAssignmentWorks (1 ms)
3: [ RUN ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/8.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/8.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/8.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/8.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/8.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/8.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/8.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/8.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/8 (1 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/9, where TypeParam = gmx::ArrayRef<double>
3: [ RUN ] ArrayRefTest/9.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/9.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/9.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/9.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/9.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/9.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/9.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/9.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/9.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/9.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/9 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/10, where TypeParam = gmx::ArrayRef<char const>
3: [ RUN ] ArrayRefTest/10.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/10.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/10.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/10.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/10.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/10.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/10.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/10.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/10.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/10.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/10 (1 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/11, where TypeParam = gmx::ArrayRef<unsigned char const>
3: [ RUN ] ArrayRefTest/11.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/11.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/11.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/11.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/11.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/11.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/11.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/11.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/11.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/11.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/11 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/12, where TypeParam = gmx::ArrayRef<int const>
3: [ RUN ] ArrayRefTest/12.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/12.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/12.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/12.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/12.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/12.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/12.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/12.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/12.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/12.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/12 (1 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/13, where TypeParam = gmx::ArrayRef<unsigned int const>
3: [ RUN ] ArrayRefTest/13.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/13.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/13.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/13.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/13.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/13.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/13.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/13.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/13.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/13.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/13 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/14, where TypeParam = gmx::ArrayRef<long const>
3: [ RUN ] ArrayRefTest/14.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/14.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/14.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/14.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/14.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/14.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/14.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/14.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/14.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/14.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/14 (1 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/15, where TypeParam = gmx::ArrayRef<unsigned long const>
3: [ RUN ] ArrayRefTest/15.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/15.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/15.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/15.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/15.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/15.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/15.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/15.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/15.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/15.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/15 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/16, where TypeParam = gmx::ArrayRef<long long const>
3: [ RUN ] ArrayRefTest/16.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/16.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/16.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/16.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/16.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/16.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/16.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/16.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/16.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/16.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/16 (1 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/17, where TypeParam = gmx::ArrayRef<unsigned long long const>
3: [ RUN ] ArrayRefTest/17.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/17.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/17.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/17.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/17.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/17.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/17.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/17.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/17.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/17.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/17 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/18, where TypeParam = gmx::ArrayRef<float const>
3: [ RUN ] ArrayRefTest/18.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/18.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/18.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/18.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/18.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/18.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/18.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/18.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/18.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/18.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/18 (1 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/19, where TypeParam = gmx::ArrayRef<double const>
3: [ RUN ] ArrayRefTest/19.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/19.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/19.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/19.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/19.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/19.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/19.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/19.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/19.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/19.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/19 (0 ms total)
3:
3: [----------] 2 tests from CStringUtilityTest
3: [ RUN ] CStringUtilityTest.CaseInsensitiveComparison
3: [ OK ] CStringUtilityTest.CaseInsensitiveComparison (0 ms)
3: [ RUN ] CStringUtilityTest.CaseInsensitiveComparisonInLength
3: [ OK ] CStringUtilityTest.CaseInsensitiveComparisonInLength (0 ms)
3: [----------] 2 tests from CStringUtilityTest (0 ms total)
3:
3: [----------] 2 tests from DefaultInitializationAllocator
3: [ RUN ] DefaultInitializationAllocator.PerformsValueInitialization
3: [ OK ] DefaultInitializationAllocator.PerformsValueInitialization (0 ms)
3: [ RUN ] DefaultInitializationAllocator.PerformsNoInitialization
3: [ OK ] DefaultInitializationAllocator.PerformsNoInitialization (0 ms)
3: [----------] 2 tests from DefaultInitializationAllocator (0 ms total)
3:
3: [----------] 4 tests from EnumerationHelpersTest
3: [ RUN ] EnumerationHelpersTest.EnumerationWrapperWorks
3: [ OK ] EnumerationHelpersTest.EnumerationWrapperWorks (0 ms)
3: [ RUN ] EnumerationHelpersTest.EnumerationArrayWorks
3: [ OK ] EnumerationHelpersTest.EnumerationArrayWorks (0 ms)
3: [ RUN ] EnumerationHelpersTest.EnumerationArrayCountIsSafe
3: [ OK ] EnumerationHelpersTest.EnumerationArrayCountIsSafe (0 ms)
3: [ RUN ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks
3: [ OK ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks (0 ms)
3: [----------] 4 tests from EnumerationHelpersTest (1 ms total)
3:
3: [----------] 9 tests from FixedCapacityVectorTest
3: [ RUN ] FixedCapacityVectorTest.IsEmpty
3: [ OK ] FixedCapacityVectorTest.IsEmpty (0 ms)
3: [ RUN ] FixedCapacityVectorTest.PushWorks
3: [ OK ] FixedCapacityVectorTest.PushWorks (0 ms)
3: [ RUN ] FixedCapacityVectorTest.PopWorks
3: [ OK ] FixedCapacityVectorTest.PopWorks (0 ms)
3: [ RUN ] FixedCapacityVectorTest.ClearWorks
3: [ OK ] FixedCapacityVectorTest.ClearWorks (0 ms)
3: [ RUN ] FixedCapacityVectorTest.EmplaceBackWorks
3: [ OK ] FixedCapacityVectorTest.EmplaceBackWorks (0 ms)
3: [ RUN ] FixedCapacityVectorTest.AtThrows
3: [ OK ] FixedCapacityVectorTest.AtThrows (1 ms)
3: [ RUN ] FixedCapacityVectorTest.IteratorWorks
3: [ OK ] FixedCapacityVectorTest.IteratorWorks (0 ms)
3: [ RUN ] FixedCapacityVectorTest.ReverseIteratorWorks
3: [ OK ] FixedCapacityVectorTest.ReverseIteratorWorks (0 ms)
3: [ RUN ] FixedCapacityVectorTest.ZeroCapacityWorks
3: [ OK ] FixedCapacityVectorTest.ZeroCapacityWorks (0 ms)
3: [----------] 9 tests from FixedCapacityVectorTest (1 ms total)
3:
3: [----------] 5 tests from InMemorySerializerTest
3: [ RUN ] InMemorySerializerTest.Roundtrip
3: [ OK ] InMemorySerializerTest.Roundtrip (0 ms)
3: [ RUN ] InMemorySerializerTest.RoundtripWithEndianessSwap
3: [ OK ] InMemorySerializerTest.RoundtripWithEndianessSwap (0 ms)
3: [ RUN ] InMemorySerializerTest.SerializerExplicitEndianessSwap
3: [ OK ] InMemorySerializerTest.SerializerExplicitEndianessSwap (0 ms)
3: [ RUN ] InMemorySerializerTest.DeserializerExplicitEndianessSwap
3: [ OK ] InMemorySerializerTest.DeserializerExplicitEndianessSwap (0 ms)
3: [ RUN ] InMemorySerializerTest.SizeIsCorrect
3: [ OK ] InMemorySerializerTest.SizeIsCorrect (0 ms)
3: [----------] 5 tests from InMemorySerializerTest (0 ms total)
3:
3: [----------] 4 tests from KeyValueTreeSerializerTest
3: [ RUN ] KeyValueTreeSerializerTest.EmptyTree
3: [ OK ] KeyValueTreeSerializerTest.EmptyTree (1 ms)
3: [ RUN ] KeyValueTreeSerializerTest.SimpleObject
3: [ OK ] KeyValueTreeSerializerTest.SimpleObject (1 ms)
3: [ RUN ] KeyValueTreeSerializerTest.ObjectWithArrays
3: [ OK ] KeyValueTreeSerializerTest.ObjectWithArrays (0 ms)
3: [ RUN ] KeyValueTreeSerializerTest.ObjectWithObjects
3: [ OK ] KeyValueTreeSerializerTest.ObjectWithObjects (0 ms)
3: [----------] 4 tests from KeyValueTreeSerializerTest (3 ms total)
3:
3: [----------] 6 tests from TreeValueTransformTest
3: [ RUN ] TreeValueTransformTest.SimpleTransforms
3: [ OK ] TreeValueTransformTest.SimpleTransforms (1 ms)
3: [ RUN ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive
3: [ OK ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive (1 ms)
3: [ RUN ] TreeValueTransformTest.SimpleTransformsToObject
3: [ OK ] TreeValueTransformTest.SimpleTransformsToObject (0 ms)
3: [ RUN ] TreeValueTransformTest.ObjectFromString
3: [ OK ] TreeValueTransformTest.ObjectFromString (1 ms)
3: [ RUN ] TreeValueTransformTest.ObjectFromMultipleStrings
3: [ OK ] TreeValueTransformTest.ObjectFromMultipleStrings (0 ms)
3: [ RUN ] TreeValueTransformTest.ScopedTransformRules
3: [ OK ] TreeValueTransformTest.ScopedTransformRules (1 ms)
3: [----------] 6 tests from TreeValueTransformTest (4 ms total)
3:
3: [----------] 1 test from TreeValueTransformErrorTest
3: [ RUN ] TreeValueTransformErrorTest.ConversionError
3: [ OK ] TreeValueTransformErrorTest.ConversionError (1 ms)
3: [----------] 1 test from TreeValueTransformErrorTest (1 ms total)
3:
3: [----------] 7 tests from LoggerTest
3: [ RUN ] LoggerTest.EmptyLoggerWorks
3: [ OK ] LoggerTest.EmptyLoggerWorks (0 ms)
3: [ RUN ] LoggerTest.LogsToStream
3: [ OK ] LoggerTest.LogsToStream (0 ms)
3: [ RUN ] LoggerTest.LogsToFile
3: [ OK ] LoggerTest.LogsToFile (2 ms)
3: [ RUN ] LoggerTest.LevelFilteringWorks
3: [ OK ] LoggerTest.LevelFilteringWorks (0 ms)
3: [ RUN ] LoggerTest.LogsToMultipleStreams
3: [ OK ] LoggerTest.LogsToMultipleStreams (8 ms)
3: [ RUN ] LoggerTest.LogsToMultipleFiles
3: [ OK ] LoggerTest.LogsToMultipleFiles (4 ms)
3: [ RUN ] LoggerTest.LogsToStreamAndFile
3: [ OK ] LoggerTest.LogsToStreamAndFile (1 ms)
3: [----------] 7 tests from LoggerTest (15 ms total)
3:
3: [----------] 4 tests from MutexBasicTest
3: [ RUN ] MutexBasicTest.CanBeMade
3: [ OK ] MutexBasicTest.CanBeMade (0 ms)
3: [ RUN ] MutexBasicTest.CanBeLocked
3: [ OK ] MutexBasicTest.CanBeLocked (0 ms)
3: [ RUN ] MutexBasicTest.CanBeTryLocked
3: [ OK ] MutexBasicTest.CanBeTryLocked (0 ms)
3: [ RUN ] MutexBasicTest.CanBeUsedInLockGuard
3: [ OK ] MutexBasicTest.CanBeUsedInLockGuard (0 ms)
3: [----------] 4 tests from MutexBasicTest (0 ms total)
3:
3: [----------] 3 tests from MutexTaskTest
3: [ RUN ] MutexTaskTest.MutualExclusionWorksWithLock
3: [ OK ] MutexTaskTest.MutualExclusionWorksWithLock (4 ms)
3: [ RUN ] MutexTaskTest.MutualExclusionWorksWithTryLockOnOtherThread
3: [ OK ] MutexTaskTest.MutualExclusionWorksWithTryLockOnOtherThread (0 ms)
3: [ RUN ] MutexTaskTest.MutualExclusionWorksWithTryLockOnSameThread
3: [ OK ] MutexTaskTest.MutualExclusionWorksWithTryLockOnSameThread (0 ms)
3: [----------] 3 tests from MutexTaskTest (5 ms total)
3:
3: [----------] 2 tests from PathTest
3: [ RUN ] PathTest.StripSourcePrefixWorks
3: [ OK ] PathTest.StripSourcePrefixWorks (0 ms)
3: [ RUN ] PathTest.SearchOperationsWork
3: [ OK ] PathTest.SearchOperationsWork (1 ms)
3: [----------] 2 tests from PathTest (1 ms total)
3:
3: [----------] 2 tests from PhysicalNodeCommunicatorTest
3: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct
3: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (0 ms)
3: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier
3: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (1 ms)
3: [----------] 2 tests from PhysicalNodeCommunicatorTest (1 ms total)
3:
3: [----------] 9 tests from StringUtilityTest
3: [ RUN ] StringUtilityTest.StartsWith
3: [ OK ] StringUtilityTest.StartsWith (0 ms)
3: [ RUN ] StringUtilityTest.EndsWith
3: [ OK ] StringUtilityTest.EndsWith (0 ms)
3: [ RUN ] StringUtilityTest.StripSuffixIfPresent
3: [ OK ] StringUtilityTest.StripSuffixIfPresent (0 ms)
3: [ RUN ] StringUtilityTest.StripString
3: [ OK ] StringUtilityTest.StripString (0 ms)
3: [ RUN ] StringUtilityTest.SplitString
3: [ OK ] StringUtilityTest.SplitString (0 ms)
3: [ RUN ] StringUtilityTest.SplitDelimitedString
3: [ OK ] StringUtilityTest.SplitDelimitedString (1 ms)
3: [ RUN ] StringUtilityTest.SplitAndTrimDelimitedString
3: [ OK ] StringUtilityTest.SplitAndTrimDelimitedString (1 ms)
3: [ RUN ] StringUtilityTest.CanCompareCaseInsensitive
3: [ OK ] StringUtilityTest.CanCompareCaseInsensitive (0 ms)
3: [ RUN ] StringUtilityTest.CanCompareCaseInsensitiveInLength
3: [ OK ] StringUtilityTest.CanCompareCaseInsensitiveInLength (0 ms)
3: [----------] 9 tests from StringUtilityTest (2 ms total)
3:
3: [----------] 2 tests from FormatStringTest
3: [ RUN ] FormatStringTest.HandlesBasicFormatting
3: [ OK ] FormatStringTest.HandlesBasicFormatting (0 ms)
3: [ RUN ] FormatStringTest.HandlesLongStrings
3: [ OK ] FormatStringTest.HandlesLongStrings (0 ms)
3: [----------] 2 tests from FormatStringTest (0 ms total)
3:
3: [----------] 1 test from StringFormatterTest
3: [ RUN ] StringFormatterTest.HandlesBasicFormatting
3: [ OK ] StringFormatterTest.HandlesBasicFormatting (1 ms)
3: [----------] 1 test from StringFormatterTest (1 ms total)
3:
3: [----------] 1 test from formatAndJoinTest
3: [ RUN ] formatAndJoinTest.Works
3: [ OK ] formatAndJoinTest.Works (0 ms)
3: [----------] 1 test from formatAndJoinTest (0 ms total)
3:
3: [----------] 1 test from JoinStringsTest
3: [ RUN ] JoinStringsTest.Works
3: [ OK ] JoinStringsTest.Works (0 ms)
3: [----------] 1 test from JoinStringsTest (0 ms total)
3:
3: [----------] 6 tests from ReplaceAllTest
3: [ RUN ] ReplaceAllTest.HandlesEmptyStrings
3: [ OK ] ReplaceAllTest.HandlesEmptyStrings (0 ms)
3: [ RUN ] ReplaceAllTest.HandlesNoMatches
3: [ OK ] ReplaceAllTest.HandlesNoMatches (0 ms)
3: [ RUN ] ReplaceAllTest.HandlesMatchesAtEnds
3: [ OK ] ReplaceAllTest.HandlesMatchesAtEnds (0 ms)
3: [ RUN ] ReplaceAllTest.HandlesMultipleMatches
3: [ OK ] ReplaceAllTest.HandlesMultipleMatches (0 ms)
3: [ RUN ] ReplaceAllTest.HandlesWordBoundaries
3: [ OK ] ReplaceAllTest.HandlesWordBoundaries (0 ms)
3: [ RUN ] ReplaceAllTest.HandlesPossibleRecursiveMatches
3: [ OK ] ReplaceAllTest.HandlesPossibleRecursiveMatches (0 ms)
3: [----------] 6 tests from ReplaceAllTest (0 ms total)
3:
3: [----------] 10 tests from TextLineWrapperTest
3: [ RUN ] TextLineWrapperTest.HandlesEmptyStrings
3: [ OK ] TextLineWrapperTest.HandlesEmptyStrings (0 ms)
3: [ RUN ] TextLineWrapperTest.HandlesTrailingWhitespace
3: [ OK ] TextLineWrapperTest.HandlesTrailingWhitespace (0 ms)
3: [ RUN ] TextLineWrapperTest.HandlesTrailingNewlines
3: [ OK ] TextLineWrapperTest.HandlesTrailingNewlines (0 ms)
3: [ RUN ] TextLineWrapperTest.WrapsCorrectly
3: [ OK ] TextLineWrapperTest.WrapsCorrectly (0 ms)
3: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks
3: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks (1 ms)
3: [ RUN ] TextLineWrapperTest.HandlesIndent
3: [ OK ] TextLineWrapperTest.HandlesIndent (0 ms)
3: [ RUN ] TextLineWrapperTest.HandlesIndentWithEmptyLines
3: [ OK ] TextLineWrapperTest.HandlesIndentWithEmptyLines (1 ms)
3: [ RUN ] TextLineWrapperTest.HandlesHangingIndent
3: [ OK ] TextLineWrapperTest.HandlesHangingIndent (0 ms)
3: [ RUN ] TextLineWrapperTest.HandlesContinuationCharacter
3: [ OK ] TextLineWrapperTest.HandlesContinuationCharacter (0 ms)
3: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace
3: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace (1 ms)
3: [----------] 10 tests from TextLineWrapperTest (4 ms total)
3:
3: [----------] 6 tests from TextWriterTest
3: [ RUN ] TextWriterTest.WritesLines
3: [ OK ] TextWriterTest.WritesLines (0 ms)
3: [ RUN ] TextWriterTest.WritesLinesInParts
3: [ OK ] TextWriterTest.WritesLinesInParts (1 ms)
3: [ RUN ] TextWriterTest.WritesWrappedLines
3: [ OK ] TextWriterTest.WritesWrappedLines (0 ms)
3: [ RUN ] TextWriterTest.WritesLinesInPartsWithWrapper
3: [ OK ] TextWriterTest.WritesLinesInPartsWithWrapper (0 ms)
3: [ RUN ] TextWriterTest.TracksNewlines
3: [ OK ] TextWriterTest.TracksNewlines (1 ms)
3: [ RUN ] TextWriterTest.PreservesTrailingWhitespace
3: [ OK ] TextWriterTest.PreservesTrailingWhitespace (0 ms)
3: [----------] 6 tests from TextWriterTest (2 ms total)
3:
3: [----------] 1 test from TypeTraitsTest
3: [ RUN ] TypeTraitsTest.IsIntegralConstant
3: [ OK ] TypeTraitsTest.IsIntegralConstant (0 ms)
3: [----------] 1 test from TypeTraitsTest (0 ms total)
3:
3: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32
3: [ RUN ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0
3: [ OK ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 (0 ms)
3: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitBit/0
3: [ OK ] BitmaskTest32_11/BitmaskTest32.InitBit/0 (0 ms)
3: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0
3: [ OK ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 (0 ms)
3: [ RUN ] BitmaskTest32_11/BitmaskTest32.Disjoint/0
3: [ OK ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 (0 ms)
3: [ RUN ] BitmaskTest32_11/BitmaskTest32.Union/0
3: [ OK ] BitmaskTest32_11/BitmaskTest32.Union/0 (0 ms)
3: [ RUN ] BitmaskTest32_11/BitmaskTest32.ToHex/0
3: [ OK ] BitmaskTest32_11/BitmaskTest32.ToHex/0 (0 ms)
3: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 (1 ms total)
3:
3: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/0
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/0 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/1
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/1 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 (0 ms)
3: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 (0 ms total)
3:
3: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/0
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/0 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/1
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/1 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 (0 ms)
3: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 (1 ms total)
3:
3: [----------] 9 tests from WithAndWithoutMutex/DifferentTasksTest
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/0
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/0 (0 ms)
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/1
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/1 (1 ms)
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/2
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/2 (0 ms)
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/0
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/0 (0 ms)
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/1
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/1 (1 ms)
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/2
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/2 (0 ms)
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/0
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/0 (0 ms)
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/1
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/1 (0 ms)
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/2
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/2 (0 ms)
3: [----------] 9 tests from WithAndWithoutMutex/DifferentTasksTest (2 ms total)
3:
3: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest
3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0
3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 (1 ms)
3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1
3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 (0 ms)
3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2
3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 (0 ms)
3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3
3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 (1 ms)
3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4
3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 (0 ms)
3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5
3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 (0 ms)
3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6
3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 (1 ms)
3: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest (3 ms total)
3:
3: [----------] Global test environment tear-down
3: [==========] 347 tests from 56 test cases ran. (65 ms total)
3: [ PASSED ] 347 tests.
3/52 Test #3: UtilityUnitTests .................... Passed 0.19 sec
test 4
Start 4: UtilityMpiUnitTests
4: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/utility-mpi-test "-ntmpi" "4" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/UtilityMpiUnitTests.xml"
4: Test timeout computed to be: 30
4: [==========] Running 2 tests from 1 test case.
4: [----------] Global test environment set-up.
4: [----------] 2 tests from PhysicalNodeCommunicatorTest
4: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct
4: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (2 ms)
4: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier
4: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (1 ms)
4: [----------] 2 tests from PhysicalNodeCommunicatorTest (4 ms total)
4:
4: [----------] Global test environment tear-down
4: [==========] 2 tests from 1 test case ran. (5 ms total)
4: [ PASSED ] 2 tests.
4/52 Test #4: UtilityMpiUnitTests ................. Passed 0.07 sec
test 5
Start 5: MdlibUnitTest
5: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdlib-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdlibUnitTest.xml"
5: Test timeout computed to be: 30
5: [==========] Running 149 tests from 11 test cases.
5: [----------] Global test environment set-up.
5: [----------] 1 test from VerletBufferConstraintTest
5: [ RUN ] VerletBufferConstraintTest.EqualMasses
5: [ OK ] VerletBufferConstraintTest.EqualMasses (0 ms)
5: [----------] 1 test from VerletBufferConstraintTest (1 ms total)
5:
5: [----------] 2 tests from PrEbinTest
5: [ RUN ] PrEbinTest.HandlesAverages
5: [ OK ] PrEbinTest.HandlesAverages (2 ms)
5: [ RUN ] PrEbinTest.HandlesEmptyAverages
5: [ OK ] PrEbinTest.HandlesEmptyAverages (1 ms)
5: [----------] 2 tests from PrEbinTest (5 ms total)
5:
5: [----------] 4 tests from ShakeTest
5: [ RUN ] ShakeTest.ConstrainsOneBond
5: [ OK ] ShakeTest.ConstrainsOneBond (0 ms)
5: [ RUN ] ShakeTest.ConstrainsTwoDisjointBonds
5: [ OK ] ShakeTest.ConstrainsTwoDisjointBonds (0 ms)
5: [ RUN ] ShakeTest.ConstrainsTwoBondsWithACommonAtom
5: [ OK ] ShakeTest.ConstrainsTwoBondsWithACommonAtom (0 ms)
5: [ RUN ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms
5: [ OK ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms (0 ms)
5: [----------] 4 tests from ShakeTest (1 ms total)
5:
5: [----------] 1 test from NullSignalTest
5: [ RUN ] NullSignalTest.NullSignallerWorks
5: [ OK ] NullSignalTest.NullSignallerWorks (0 ms)
5: [----------] 1 test from NullSignalTest (0 ms total)
5:
5: [----------] 7 tests from SignalTest
5: [ RUN ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace
5: [ OK ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace (0 ms)
5: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace
5: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace (0 ms)
5: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace
5: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace (0 ms)
5: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace
5: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace (0 ms)
5: [ RUN ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace
5: [ OK ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace (1 ms)
5: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace
5: [ OK ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace (0 ms)
5: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace
5: [ OK ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace (0 ms)
5: [----------] 7 tests from SignalTest (2 ms total)
5:
5: [----------] 9 tests from UpdateGroups
5: [ RUN ] UpdateGroups.ethaneUA
5: [ OK ] UpdateGroups.ethaneUA (0 ms)
5: [ RUN ] UpdateGroups.methane
5: [ OK ] UpdateGroups.methane (0 ms)
5: [ RUN ] UpdateGroups.ethane
5: [ OK ] UpdateGroups.ethane (1 ms)
5: [ RUN ] UpdateGroups.butaneUA
5: [ OK ] UpdateGroups.butaneUA (0 ms)
5: [ RUN ] UpdateGroups.waterThreeSite
5: [ OK ] UpdateGroups.waterThreeSite (0 ms)
5: [ RUN ] UpdateGroups.waterFourSite
5: [ OK ] UpdateGroups.waterFourSite (0 ms)
5: [ RUN ] UpdateGroups.fourAtomsWithSettle
5: [ OK ] UpdateGroups.fourAtomsWithSettle (0 ms)
5: [ RUN ] UpdateGroups.waterFlexAngle
5: [ OK ] UpdateGroups.waterFlexAngle (0 ms)
5: [ RUN ] UpdateGroups.twoMoltypes
5: [ OK ] UpdateGroups.twoMoltypes (1 ms)
5: [----------] 9 tests from UpdateGroups (4 ms total)
5:
5: [----------] 1 test from UpdateGroupsCog
5: [ RUN ] UpdateGroupsCog.ComputesCogs
5: [ OK ] UpdateGroupsCog.ComputesCogs (11 ms)
5: [----------] 1 test from UpdateGroupsCog (11 ms total)
5:
5: [----------] 84 tests from WithParameters/ConstraintsTest
5: [ RUN ] WithParameters/ConstraintsTest.SingleConstraint/0
5: [ OK ] WithParameters/ConstraintsTest.SingleConstraint/0 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.SingleConstraint/1
5: [ OK ] WithParameters/ConstraintsTest.SingleConstraint/1 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.SingleConstraint/2
5: [ OK ] WithParameters/ConstraintsTest.SingleConstraint/2 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.SingleConstraint/3
5: [ OK ] WithParameters/ConstraintsTest.SingleConstraint/3 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/0
5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/0 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/1
5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/1 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/2
5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/2 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/3
5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/3 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/4
5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/4 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/5
5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/5 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/6
5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/6 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/7
5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/7 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/0
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/0 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/1
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/1 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/2
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/2 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/3
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/3 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/4
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/4 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/5
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/5 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/6
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/6 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/7
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/7 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/8
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/8 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/9
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/9 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/10
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/10 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/11
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/11 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/0
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/0 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/1
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/1 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/2
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/2 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/3
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/3 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/4
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/4 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/5
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/5 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/6
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/6 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/7
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/7 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/8
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/8 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/9
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/9 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/10
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/10 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/11
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/11 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/12
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/12 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/13
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/13 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/14
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/14 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/15
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/15 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/0
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/0 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/1
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/1 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/2
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/2 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/3
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/3 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/4
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/4 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/5
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/5 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/6
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/6 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/7
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/7 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/8
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/8 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/9
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/9 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/10
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/10 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/11
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/11 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/12
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/12 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/13
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/13 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/14
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/14 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/15
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/15 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/16
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/16 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/17
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/17 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/18
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/18 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/19
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/19 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/0
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/0 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/1
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/1 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/2
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/2 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/3
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/3 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/4
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/4 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/5
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/5 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/6
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/6 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/7
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/7 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/8
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/8 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/9
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/9 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/10
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/10 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/11
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/11 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/12
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/12 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/13
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/13 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/14
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/14 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/15
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/15 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/16
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/16 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/17
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/17 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/18
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/18 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/19
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/19 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/20
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/20 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/21
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/21 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/22
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/22 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/23
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/23 (0 ms)
5: [----------] 84 tests from WithParameters/ConstraintsTest (37 ms total)
5:
5: [----------] 11 tests from WithParameters/EnergyOutputTest
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/0
5: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_0.edr as double precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/0 (21 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/1
5: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_1.edr as double precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/1 (8 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/2
5: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_2.edr as double precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/2 (14 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/3
5: [ OK ] WithParameters/EnergyOutputTest.CheckOutput/3 (2 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/4
5: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_4.edr as double precision energy file
5:
Reading energy frame 0 time 10.100
Reading energy frame 1 time 27.500
Reading energy frame 2 time 44.900
Reading energy frame 3 time 62.300
Reading energy frame 4 time 79.700
Reading energy frame 5 time 97.100
Reading energy frame 6 time 114.500
Reading energy frame 7 time 131.900
Reading energy frame 8 time 149.300
Reading energy frame 9 time 166.700 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/4 (50 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/5
5: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_5.edr as double precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/5 (22 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/6
5: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_6.edr as double precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/6 (12 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/7
5: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_7.edr as double precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/7 (13 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/8
5: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_8.edr as double precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/8 (13 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/9
5: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_9.edr as double precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/9 (12 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/10
5: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_10.edr as double precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/10 (13 ms)
5: [----------] 11 tests from WithParameters/EnergyOutputTest (206 ms total)
5:
5: [----------] 16 tests from WithParameters/LeapFrogTest
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/0
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/0 (1 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/1
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/1 (1 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/2
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/2 (1 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/3
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/3 (1 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/4
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/4 (1 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/5
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/5 (16 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/6
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/6 (31 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/7
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/7 (3 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/8
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/8 (1 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/9
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/9 (1 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/10
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/10 (11 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/11
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/11 (10 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/12
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/12 (11 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/13
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/13 (11 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/14
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/14 (11 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/15
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/15 (11 ms)
5: [----------] 16 tests from WithParameters/LeapFrogTest (142 ms total)
5:
5: [----------] 13 tests from WithParameters/SettleTest
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/0
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/0 (1 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/1
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/1 (1 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/2
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/2 (1 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/3
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/3 (2 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/4
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/4 (2 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/5
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/5 (2 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/6
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/6 (3 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/7
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/7 (4 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/8
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/8 (7 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/9
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/9 (5 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/10
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/10 (4 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/11
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/11 (7 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/12
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/12 (8 ms)
5: [----------] 13 tests from WithParameters/SettleTest (52 ms total)
5:
5: [----------] Global test environment tear-down
5: [==========] 149 tests from 11 test cases ran. (464 ms total)
5: [ PASSED ] 149 tests.
5/52 Test #5: MdlibUnitTest ....................... Passed 0.56 sec
test 6
Start 6: AppliedForcesUnitTest
6: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/applied_forces-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/AppliedForcesUnitTest.xml"
6: Test timeout computed to be: 30
6: [==========] Running 20 tests from 4 test cases.
6: [----------] Global test environment set-up.
6: [----------] 2 tests from DensityFittingTest
6: [ RUN ] DensityFittingTest.ForceProviderLackingInputThrows
6: [ OK ] DensityFittingTest.ForceProviderLackingInputThrows (2 ms)
6: [ RUN ] DensityFittingTest.SingleAtom
6: [ OK ] DensityFittingTest.SingleAtom (2 ms)
6: [----------] 2 tests from DensityFittingTest (5 ms total)
6:
6: [----------] 8 tests from DensityFittingOptionsTest
6: [ RUN ] DensityFittingOptionsTest.DefaultParameters
6: [ OK ] DensityFittingOptionsTest.DefaultParameters (0 ms)
6: [ RUN ] DensityFittingOptionsTest.OptionSetsActive
6: [ OK ] DensityFittingOptionsTest.OptionSetsActive (1 ms)
6: [ RUN ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive
6: [ OK ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms)
6: [ RUN ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive
6: [ OK ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive (1 ms)
6: [ RUN ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup
6: [ OK ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup (1 ms)
6: [ RUN ] DensityFittingOptionsTest.InternalsToKvt
6: [ OK ] DensityFittingOptionsTest.InternalsToKvt (0 ms)
6: [ RUN ] DensityFittingOptionsTest.KvtToInternal
6: [ OK ] DensityFittingOptionsTest.KvtToInternal (1 ms)
6: [ RUN ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent
6: [ OK ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent (1 ms)
6: [----------] 8 tests from DensityFittingOptionsTest (7 ms total)
6:
6: [----------] 7 tests from DensityFittingAmplitudeLookupTest
6: [ RUN ] DensityFittingAmplitudeLookupTest.Unity
6: [ OK ] DensityFittingAmplitudeLookupTest.Unity (0 ms)
6: [ RUN ] DensityFittingAmplitudeLookupTest.Charge
6: [ OK ] DensityFittingAmplitudeLookupTest.Charge (0 ms)
6: [ RUN ] DensityFittingAmplitudeLookupTest.Masses
6: [ OK ] DensityFittingAmplitudeLookupTest.Masses (0 ms)
6: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyAssign
6: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyAssign (0 ms)
6: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyConstruct
6: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyConstruct (0 ms)
6: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveAssign
6: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveAssign (0 ms)
6: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveConstruct
6: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveConstruct (0 ms)
6: [----------] 7 tests from DensityFittingAmplitudeLookupTest (1 ms total)
6:
6: [----------] 3 tests from ElectricFieldTest
6: [ RUN ] ElectricFieldTest.Static
6: [ OK ] ElectricFieldTest.Static (1 ms)
6: [ RUN ] ElectricFieldTest.Oscillating
6: [ OK ] ElectricFieldTest.Oscillating (1 ms)
6: [ RUN ] ElectricFieldTest.Pulsed
6: [ OK ] ElectricFieldTest.Pulsed (0 ms)
6: [----------] 3 tests from ElectricFieldTest (2 ms total)
6:
6: [----------] Global test environment tear-down
6: [==========] 20 tests from 4 test cases ran. (18 ms total)
6: [ PASSED ] 20 tests.
6/52 Test #6: AppliedForcesUnitTest ............... Passed 0.08 sec
test 7
Start 7: ListedForcesTest
7: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/listed_forces-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/ListedForcesTest.xml"
7: Test timeout computed to be: 30
7: [==========] Running 315 tests from 5 test cases.
7: [----------] Global test environment set-up.
7: [----------] 72 tests from Bond/ListedForcesTest
7: [ RUN ] Bond/ListedForcesTest.Ifunc/0
7: [ OK ] Bond/ListedForcesTest.Ifunc/0 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/1
7: [ OK ] Bond/ListedForcesTest.Ifunc/1 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/2
7: [ OK ] Bond/ListedForcesTest.Ifunc/2 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/3
7: [ OK ] Bond/ListedForcesTest.Ifunc/3 (0 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/4
7: [ OK ] Bond/ListedForcesTest.Ifunc/4 (0 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/5
7: [ OK ] Bond/ListedForcesTest.Ifunc/5 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/6
7: [ OK ] Bond/ListedForcesTest.Ifunc/6 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/7
7: [ OK ] Bond/ListedForcesTest.Ifunc/7 (0 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/8
7: [ OK ] Bond/ListedForcesTest.Ifunc/8 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/9
7: [ OK ] Bond/ListedForcesTest.Ifunc/9 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/10
7: [ OK ] Bond/ListedForcesTest.Ifunc/10 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/11
7: [ OK ] Bond/ListedForcesTest.Ifunc/11 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/12
7: [ OK ] Bond/ListedForcesTest.Ifunc/12 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/13
7: [ OK ] Bond/ListedForcesTest.Ifunc/13 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/14
7: [ OK ] Bond/ListedForcesTest.Ifunc/14 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/15
7: [ OK ] Bond/ListedForcesTest.Ifunc/15 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/16
7: [ OK ] Bond/ListedForcesTest.Ifunc/16 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/17
7: [ OK ] Bond/ListedForcesTest.Ifunc/17 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/18
7: [ OK ] Bond/ListedForcesTest.Ifunc/18 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/19
7: [ OK ] Bond/ListedForcesTest.Ifunc/19 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/20
7: [ OK ] Bond/ListedForcesTest.Ifunc/20 (0 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/21
7: [ OK ] Bond/ListedForcesTest.Ifunc/21 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/22
7: [ OK ] Bond/ListedForcesTest.Ifunc/22 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/23
7: [ OK ] Bond/ListedForcesTest.Ifunc/23 (0 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/24
7: [ OK ] Bond/ListedForcesTest.Ifunc/24 (0 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/25
7: [ OK ] Bond/ListedForcesTest.Ifunc/25 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/26
7: [ OK ] Bond/ListedForcesTest.Ifunc/26 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/27
7: [ OK ] Bond/ListedForcesTest.Ifunc/27 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/28
7: [ OK ] Bond/ListedForcesTest.Ifunc/28 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/29
7: [ OK ] Bond/ListedForcesTest.Ifunc/29 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/30
7: [ OK ] Bond/ListedForcesTest.Ifunc/30 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/31
7: [ OK ] Bond/ListedForcesTest.Ifunc/31 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/32
7: [ OK ] Bond/ListedForcesTest.Ifunc/32 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/33
7: [ OK ] Bond/ListedForcesTest.Ifunc/33 (2 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/34
7: [ OK ] Bond/ListedForcesTest.Ifunc/34 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/35
7: [ OK ] Bond/ListedForcesTest.Ifunc/35 (2 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/36
7: [ OK ] Bond/ListedForcesTest.Ifunc/36 (0 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/37
7: [ OK ] Bond/ListedForcesTest.Ifunc/37 (0 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/38
7: [ OK ] Bond/ListedForcesTest.Ifunc/38 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/39
7: [ OK ] Bond/ListedForcesTest.Ifunc/39 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/40
7: [ OK ] Bond/ListedForcesTest.Ifunc/40 (0 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/41
7: [ OK ] Bond/ListedForcesTest.Ifunc/41 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/42
7: [ OK ] Bond/ListedForcesTest.Ifunc/42 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/43
7: [ OK ] Bond/ListedForcesTest.Ifunc/43 (0 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/44
7: [ OK ] Bond/ListedForcesTest.Ifunc/44 (0 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/45
7: [ OK ] Bond/ListedForcesTest.Ifunc/45 (2 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/46
7: [ OK ] Bond/ListedForcesTest.Ifunc/46 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/47
7: [ OK ] Bond/ListedForcesTest.Ifunc/47 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/48
7: [ OK ] Bond/ListedForcesTest.Ifunc/48 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/49
7: [ OK ] Bond/ListedForcesTest.Ifunc/49 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/50
7: [ OK ] Bond/ListedForcesTest.Ifunc/50 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/51
7: [ OK ] Bond/ListedForcesTest.Ifunc/51 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/52
7: [ OK ] Bond/ListedForcesTest.Ifunc/52 (2 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/53
7: [ OK ] Bond/ListedForcesTest.Ifunc/53 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/54
7: [ OK ] Bond/ListedForcesTest.Ifunc/54 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/55
7: [ OK ] Bond/ListedForcesTest.Ifunc/55 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/56
7: [ OK ] Bond/ListedForcesTest.Ifunc/56 (0 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/57
7: [ OK ] Bond/ListedForcesTest.Ifunc/57 (0 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/58
7: [ OK ] Bond/ListedForcesTest.Ifunc/58 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/59
7: [ OK ] Bond/ListedForcesTest.Ifunc/59 (0 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/60
7: [ OK ] Bond/ListedForcesTest.Ifunc/60 (0 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/61
7: [ OK ] Bond/ListedForcesTest.Ifunc/61 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/62
7: [ OK ] Bond/ListedForcesTest.Ifunc/62 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/63
7: [ OK ] Bond/ListedForcesTest.Ifunc/63 (0 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/64
7: [ OK ] Bond/ListedForcesTest.Ifunc/64 (0 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/65
7: [ OK ] Bond/ListedForcesTest.Ifunc/65 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/66
7: [ OK ] Bond/ListedForcesTest.Ifunc/66 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/67
7: [ OK ] Bond/ListedForcesTest.Ifunc/67 (0 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/68
7: [ OK ] Bond/ListedForcesTest.Ifunc/68 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/69
7: [ OK ] Bond/ListedForcesTest.Ifunc/69 (1 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/70
7: [ OK ] Bond/ListedForcesTest.Ifunc/70 (0 ms)
7: [ RUN ] Bond/ListedForcesTest.Ifunc/71
7: [ OK ] Bond/ListedForcesTest.Ifunc/71 (0 ms)
7: [----------] 72 tests from Bond/ListedForcesTest (72 ms total)
7:
7: [----------] 99 tests from Angle/ListedForcesTest
7: [ RUN ] Angle/ListedForcesTest.Ifunc/0
7: [ OK ] Angle/ListedForcesTest.Ifunc/0 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/1
7: [ OK ] Angle/ListedForcesTest.Ifunc/1 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/2
7: [ OK ] Angle/ListedForcesTest.Ifunc/2 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/3
7: [ OK ] Angle/ListedForcesTest.Ifunc/3 (0 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/4
7: [ OK ] Angle/ListedForcesTest.Ifunc/4 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/5
7: [ OK ] Angle/ListedForcesTest.Ifunc/5 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/6
7: [ OK ] Angle/ListedForcesTest.Ifunc/6 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/7
7: [ OK ] Angle/ListedForcesTest.Ifunc/7 (0 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/8
7: [ OK ] Angle/ListedForcesTest.Ifunc/8 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/9
7: [ OK ] Angle/ListedForcesTest.Ifunc/9 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/10
7: [ OK ] Angle/ListedForcesTest.Ifunc/10 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/11
7: [ OK ] Angle/ListedForcesTest.Ifunc/11 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/12
7: [ OK ] Angle/ListedForcesTest.Ifunc/12 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/13
7: [ OK ] Angle/ListedForcesTest.Ifunc/13 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/14
7: [ OK ] Angle/ListedForcesTest.Ifunc/14 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/15
7: [ OK ] Angle/ListedForcesTest.Ifunc/15 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/16
7: [ OK ] Angle/ListedForcesTest.Ifunc/16 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/17
7: [ OK ] Angle/ListedForcesTest.Ifunc/17 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/18
7: [ OK ] Angle/ListedForcesTest.Ifunc/18 (0 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/19
7: [ OK ] Angle/ListedForcesTest.Ifunc/19 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/20
7: [ OK ] Angle/ListedForcesTest.Ifunc/20 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/21
7: [ OK ] Angle/ListedForcesTest.Ifunc/21 (0 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/22
7: [ OK ] Angle/ListedForcesTest.Ifunc/22 (0 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/23
7: [ OK ] Angle/ListedForcesTest.Ifunc/23 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/24
7: [ OK ] Angle/ListedForcesTest.Ifunc/24 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/25
7: [ OK ] Angle/ListedForcesTest.Ifunc/25 (0 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/26
7: [ OK ] Angle/ListedForcesTest.Ifunc/26 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/27
7: [ OK ] Angle/ListedForcesTest.Ifunc/27 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/28
7: [ OK ] Angle/ListedForcesTest.Ifunc/28 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/29
7: [ OK ] Angle/ListedForcesTest.Ifunc/29 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/30
7: [ OK ] Angle/ListedForcesTest.Ifunc/30 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/31
7: [ OK ] Angle/ListedForcesTest.Ifunc/31 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/32
7: [ OK ] Angle/ListedForcesTest.Ifunc/32 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/33
7: [ OK ] Angle/ListedForcesTest.Ifunc/33 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/34
7: [ OK ] Angle/ListedForcesTest.Ifunc/34 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/35
7: [ OK ] Angle/ListedForcesTest.Ifunc/35 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/36
7: [ OK ] Angle/ListedForcesTest.Ifunc/36 (0 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/37
7: [ OK ] Angle/ListedForcesTest.Ifunc/37 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/38
7: [ OK ] Angle/ListedForcesTest.Ifunc/38 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/39
7: [ OK ] Angle/ListedForcesTest.Ifunc/39 (0 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/40
7: [ OK ] Angle/ListedForcesTest.Ifunc/40 (0 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/41
7: [ OK ] Angle/ListedForcesTest.Ifunc/41 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/42
7: [ OK ] Angle/ListedForcesTest.Ifunc/42 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/43
7: [ OK ] Angle/ListedForcesTest.Ifunc/43 (0 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/44
7: [ OK ] Angle/ListedForcesTest.Ifunc/44 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/45
7: [ OK ] Angle/ListedForcesTest.Ifunc/45 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/46
7: [ OK ] Angle/ListedForcesTest.Ifunc/46 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/47
7: [ OK ] Angle/ListedForcesTest.Ifunc/47 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/48
7: [ OK ] Angle/ListedForcesTest.Ifunc/48 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/49
7: [ OK ] Angle/ListedForcesTest.Ifunc/49 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/50
7: [ OK ] Angle/ListedForcesTest.Ifunc/50 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/51
7: [ OK ] Angle/ListedForcesTest.Ifunc/51 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/52
7: [ OK ] Angle/ListedForcesTest.Ifunc/52 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/53
7: [ OK ] Angle/ListedForcesTest.Ifunc/53 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/54
7: [ OK ] Angle/ListedForcesTest.Ifunc/54 (0 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/55
7: [ OK ] Angle/ListedForcesTest.Ifunc/55 (0 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/56
7: [ OK ] Angle/ListedForcesTest.Ifunc/56 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/57
7: [ OK ] Angle/ListedForcesTest.Ifunc/57 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/58
7: [ OK ] Angle/ListedForcesTest.Ifunc/58 (0 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/59
7: [ OK ] Angle/ListedForcesTest.Ifunc/59 (0 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/60
7: [ OK ] Angle/ListedForcesTest.Ifunc/60 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/61
7: [ OK ] Angle/ListedForcesTest.Ifunc/61 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/62
7: [ OK ] Angle/ListedForcesTest.Ifunc/62 (0 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/63
7: [ OK ] Angle/ListedForcesTest.Ifunc/63 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/64
7: [ OK ] Angle/ListedForcesTest.Ifunc/64 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/65
7: [ OK ] Angle/ListedForcesTest.Ifunc/65 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/66
7: [ OK ] Angle/ListedForcesTest.Ifunc/66 (0 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/67
7: [ OK ] Angle/ListedForcesTest.Ifunc/67 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/68
7: [ OK ] Angle/ListedForcesTest.Ifunc/68 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/69
7: [ OK ] Angle/ListedForcesTest.Ifunc/69 (0 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/70
7: [ OK ] Angle/ListedForcesTest.Ifunc/70 (0 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/71
7: [ OK ] Angle/ListedForcesTest.Ifunc/71 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/72
7: [ OK ] Angle/ListedForcesTest.Ifunc/72 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/73
7: [ OK ] Angle/ListedForcesTest.Ifunc/73 (0 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/74
7: [ OK ] Angle/ListedForcesTest.Ifunc/74 (0 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/75
7: [ OK ] Angle/ListedForcesTest.Ifunc/75 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/76
7: [ OK ] Angle/ListedForcesTest.Ifunc/76 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/77
7: [ OK ] Angle/ListedForcesTest.Ifunc/77 (0 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/78
7: [ OK ] Angle/ListedForcesTest.Ifunc/78 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/79
7: [ OK ] Angle/ListedForcesTest.Ifunc/79 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/80
7: [ OK ] Angle/ListedForcesTest.Ifunc/80 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/81
7: [ OK ] Angle/ListedForcesTest.Ifunc/81 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/82
7: [ OK ] Angle/ListedForcesTest.Ifunc/82 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/83
7: [ OK ] Angle/ListedForcesTest.Ifunc/83 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/84
7: [ OK ] Angle/ListedForcesTest.Ifunc/84 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/85
7: [ OK ] Angle/ListedForcesTest.Ifunc/85 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/86
7: [ OK ] Angle/ListedForcesTest.Ifunc/86 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/87
7: [ OK ] Angle/ListedForcesTest.Ifunc/87 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/88
7: [ OK ] Angle/ListedForcesTest.Ifunc/88 (2 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/89
7: [ OK ] Angle/ListedForcesTest.Ifunc/89 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/90
7: [ OK ] Angle/ListedForcesTest.Ifunc/90 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/91
7: [ OK ] Angle/ListedForcesTest.Ifunc/91 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/92
7: [ OK ] Angle/ListedForcesTest.Ifunc/92 (0 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/93
7: [ OK ] Angle/ListedForcesTest.Ifunc/93 (0 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/94
7: [ OK ] Angle/ListedForcesTest.Ifunc/94 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/95
7: [ OK ] Angle/ListedForcesTest.Ifunc/95 (1 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/96
7: [ OK ] Angle/ListedForcesTest.Ifunc/96 (0 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/97
7: [ OK ] Angle/ListedForcesTest.Ifunc/97 (0 ms)
7: [ RUN ] Angle/ListedForcesTest.Ifunc/98
7: [ OK ] Angle/ListedForcesTest.Ifunc/98 (1 ms)
7: [----------] 99 tests from Angle/ListedForcesTest (101 ms total)
7:
7: [----------] 54 tests from Dihedral/ListedForcesTest
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/0
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/0 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/1
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/1 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/2
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/2 (2 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/3
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/3 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/4
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/4 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/5
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/5 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/6
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/6 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/7
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/7 (2 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/8
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/8 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/9
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/9 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/10
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/10 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/11
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/11 (0 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/12
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/12 (0 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/13
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/13 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/14
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/14 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/15
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/15 (0 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/16
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/16 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/17
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/17 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/18
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/18 (0 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/19
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/19 (0 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/20
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/20 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/21
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/21 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/22
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/22 (0 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/23
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/23 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/24
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/24 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/25
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/25 (0 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/26
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/26 (0 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/27
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/27 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/28
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/28 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/29
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/29 (2 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/30
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/30 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/31
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/31 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/32
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/32 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/33
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/33 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/34
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/34 (2 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/35
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/35 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/36
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/36 (2 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/37
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/37 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/38
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/38 (2 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/39
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/39 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/40
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/40 (2 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/41
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/41 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/42
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/42 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/43
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/43 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/44
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/44 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/45
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/45 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/46
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/46 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/47
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/47 (0 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/48
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/48 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/49
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/49 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/50
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/50 (0 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/51
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/51 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/52
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/52 (1 ms)
7: [ RUN ] Dihedral/ListedForcesTest.Ifunc/53
7: [ OK ] Dihedral/ListedForcesTest.Ifunc/53 (0 ms)
7: [----------] 54 tests from Dihedral/ListedForcesTest (58 ms total)
7:
7: [----------] 36 tests from Polarize/ListedForcesTest
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/0
7: [ OK ] Polarize/ListedForcesTest.Ifunc/0 (0 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/1
7: [ OK ] Polarize/ListedForcesTest.Ifunc/1 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/2
7: [ OK ] Polarize/ListedForcesTest.Ifunc/2 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/3
7: [ OK ] Polarize/ListedForcesTest.Ifunc/3 (0 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/4
7: [ OK ] Polarize/ListedForcesTest.Ifunc/4 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/5
7: [ OK ] Polarize/ListedForcesTest.Ifunc/5 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/6
7: [ OK ] Polarize/ListedForcesTest.Ifunc/6 (0 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/7
7: [ OK ] Polarize/ListedForcesTest.Ifunc/7 (0 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/8
7: [ OK ] Polarize/ListedForcesTest.Ifunc/8 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/9
7: [ OK ] Polarize/ListedForcesTest.Ifunc/9 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/10
7: [ OK ] Polarize/ListedForcesTest.Ifunc/10 (0 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/11
7: [ OK ] Polarize/ListedForcesTest.Ifunc/11 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/12
7: [ OK ] Polarize/ListedForcesTest.Ifunc/12 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/13
7: [ OK ] Polarize/ListedForcesTest.Ifunc/13 (0 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/14
7: [ OK ] Polarize/ListedForcesTest.Ifunc/14 (0 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/15
7: [ OK ] Polarize/ListedForcesTest.Ifunc/15 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/16
7: [ OK ] Polarize/ListedForcesTest.Ifunc/16 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/17
7: [ OK ] Polarize/ListedForcesTest.Ifunc/17 (0 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/18
7: [ OK ] Polarize/ListedForcesTest.Ifunc/18 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/19
7: [ OK ] Polarize/ListedForcesTest.Ifunc/19 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/20
7: [ OK ] Polarize/ListedForcesTest.Ifunc/20 (0 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/21
7: [ OK ] Polarize/ListedForcesTest.Ifunc/21 (0 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/22
7: [ OK ] Polarize/ListedForcesTest.Ifunc/22 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/23
7: [ OK ] Polarize/ListedForcesTest.Ifunc/23 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/24
7: [ OK ] Polarize/ListedForcesTest.Ifunc/24 (0 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/25
7: [ OK ] Polarize/ListedForcesTest.Ifunc/25 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/26
7: [ OK ] Polarize/ListedForcesTest.Ifunc/26 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/27
7: [ OK ] Polarize/ListedForcesTest.Ifunc/27 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/28
7: [ OK ] Polarize/ListedForcesTest.Ifunc/28 (0 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/29
7: [ OK ] Polarize/ListedForcesTest.Ifunc/29 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/30
7: [ OK ] Polarize/ListedForcesTest.Ifunc/30 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/31
7: [ OK ] Polarize/ListedForcesTest.Ifunc/31 (0 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/32
7: [ OK ] Polarize/ListedForcesTest.Ifunc/32 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/33
7: [ OK ] Polarize/ListedForcesTest.Ifunc/33 (1 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/34
7: [ OK ] Polarize/ListedForcesTest.Ifunc/34 (0 ms)
7: [ RUN ] Polarize/ListedForcesTest.Ifunc/35
7: [ OK ] Polarize/ListedForcesTest.Ifunc/35 (0 ms)
7: [----------] 36 tests from Polarize/ListedForcesTest (25 ms total)
7:
7: [----------] 54 tests from Restraints/ListedForcesTest
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/0
7: [ OK ] Restraints/ListedForcesTest.Ifunc/0 (2 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/1
7: [ OK ] Restraints/ListedForcesTest.Ifunc/1 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/2
7: [ OK ] Restraints/ListedForcesTest.Ifunc/2 (2 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/3
7: [ OK ] Restraints/ListedForcesTest.Ifunc/3 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/4
7: [ OK ] Restraints/ListedForcesTest.Ifunc/4 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/5
7: [ OK ] Restraints/ListedForcesTest.Ifunc/5 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/6
7: [ OK ] Restraints/ListedForcesTest.Ifunc/6 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/7
7: [ OK ] Restraints/ListedForcesTest.Ifunc/7 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/8
7: [ OK ] Restraints/ListedForcesTest.Ifunc/8 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/9
7: [ OK ] Restraints/ListedForcesTest.Ifunc/9 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/10
7: [ OK ] Restraints/ListedForcesTest.Ifunc/10 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/11
7: [ OK ] Restraints/ListedForcesTest.Ifunc/11 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/12
7: [ OK ] Restraints/ListedForcesTest.Ifunc/12 (0 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/13
7: [ OK ] Restraints/ListedForcesTest.Ifunc/13 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/14
7: [ OK ] Restraints/ListedForcesTest.Ifunc/14 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/15
7: [ OK ] Restraints/ListedForcesTest.Ifunc/15 (0 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/16
7: [ OK ] Restraints/ListedForcesTest.Ifunc/16 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/17
7: [ OK ] Restraints/ListedForcesTest.Ifunc/17 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/18
7: [ OK ] Restraints/ListedForcesTest.Ifunc/18 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/19
7: [ OK ] Restraints/ListedForcesTest.Ifunc/19 (2 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/20
7: [ OK ] Restraints/ListedForcesTest.Ifunc/20 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/21
7: [ OK ] Restraints/ListedForcesTest.Ifunc/21 (2 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/22
7: [ OK ] Restraints/ListedForcesTest.Ifunc/22 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/23
7: [ OK ] Restraints/ListedForcesTest.Ifunc/23 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/24
7: [ OK ] Restraints/ListedForcesTest.Ifunc/24 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/25
7: [ OK ] Restraints/ListedForcesTest.Ifunc/25 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/26
7: [ OK ] Restraints/ListedForcesTest.Ifunc/26 (2 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/27
7: [ OK ] Restraints/ListedForcesTest.Ifunc/27 (0 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/28
7: [ OK ] Restraints/ListedForcesTest.Ifunc/28 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/29
7: [ OK ] Restraints/ListedForcesTest.Ifunc/29 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/30
7: [ OK ] Restraints/ListedForcesTest.Ifunc/30 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/31
7: [ OK ] Restraints/ListedForcesTest.Ifunc/31 (0 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/32
7: [ OK ] Restraints/ListedForcesTest.Ifunc/32 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/33
7: [ OK ] Restraints/ListedForcesTest.Ifunc/33 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/34
7: [ OK ] Restraints/ListedForcesTest.Ifunc/34 (0 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/35
7: [ OK ] Restraints/ListedForcesTest.Ifunc/35 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/36
7: [ OK ] Restraints/ListedForcesTest.Ifunc/36 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/37
7: [ OK ] Restraints/ListedForcesTest.Ifunc/37 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/38
7: [ OK ] Restraints/ListedForcesTest.Ifunc/38 (0 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/39
7: [ OK ] Restraints/ListedForcesTest.Ifunc/39 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/40
7: [ OK ] Restraints/ListedForcesTest.Ifunc/40 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/41
7: [ OK ] Restraints/ListedForcesTest.Ifunc/41 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/42
7: [ OK ] Restraints/ListedForcesTest.Ifunc/42 (0 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/43
7: [ OK ] Restraints/ListedForcesTest.Ifunc/43 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/44
7: [ OK ] Restraints/ListedForcesTest.Ifunc/44 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/45
7: [ OK ] Restraints/ListedForcesTest.Ifunc/45 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/46
7: [ OK ] Restraints/ListedForcesTest.Ifunc/46 (2 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/47
7: [ OK ] Restraints/ListedForcesTest.Ifunc/47 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/48
7: [ OK ] Restraints/ListedForcesTest.Ifunc/48 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/49
7: [ OK ] Restraints/ListedForcesTest.Ifunc/49 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/50
7: [ OK ] Restraints/ListedForcesTest.Ifunc/50 (2 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/51
7: [ OK ] Restraints/ListedForcesTest.Ifunc/51 (1 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/52
7: [ OK ] Restraints/ListedForcesTest.Ifunc/52 (2 ms)
7: [ RUN ] Restraints/ListedForcesTest.Ifunc/53
7: [ OK ] Restraints/ListedForcesTest.Ifunc/53 (1 ms)
7: [----------] 54 tests from Restraints/ListedForcesTest (59 ms total)
7:
7: [----------] Global test environment tear-down
7: [==========] 315 tests from 5 test cases ran. (318 ms total)
7: [ PASSED ] 315 tests.
7/52 Test #7: ListedForcesTest .................... Passed 0.55 sec
test 8
Start 8: CommandLineUnitTests
8: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/commandline-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/CommandLineUnitTests.xml"
8: Test timeout computed to be: 30
8: [==========] Running 59 tests from 7 test cases.
8: [----------] Global test environment set-up.
8: [----------] 3 tests from CommandLineHelpModuleTest
8: [ RUN ] CommandLineHelpModuleTest.PrintsGeneralHelp
8: [ OK ] CommandLineHelpModuleTest.PrintsGeneralHelp (6 ms)
8: [ RUN ] CommandLineHelpModuleTest.PrintsHelpOnTopic
8: [ OK ] CommandLineHelpModuleTest.PrintsHelpOnTopic (1 ms)
8: [ RUN ] CommandLineHelpModuleTest.ExportsHelp
8: [ OK ] CommandLineHelpModuleTest.ExportsHelp (6 ms)
8: [----------] 3 tests from CommandLineHelpModuleTest (13 ms total)
8:
8: [----------] 7 tests from CommandLineHelpWriterTest
8: [ RUN ] CommandLineHelpWriterTest.HandlesOptionTypes
8: [ OK ] CommandLineHelpWriterTest.HandlesOptionTypes (3 ms)
8: [ RUN ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables
8: [ OK ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables (1 ms)
8: [ RUN ] CommandLineHelpWriterTest.HandlesLongFileOptions
8: [ OK ] CommandLineHelpWriterTest.HandlesLongFileOptions (1 ms)
8: [ RUN ] CommandLineHelpWriterTest.HandlesLongOptions
8: [ OK ] CommandLineHelpWriterTest.HandlesLongOptions (1 ms)
8: [ RUN ] CommandLineHelpWriterTest.HandlesOptionGroups
8: [ OK ] CommandLineHelpWriterTest.HandlesOptionGroups (1 ms)
8: [ RUN ] CommandLineHelpWriterTest.HandlesHelpText
8: [ OK ] CommandLineHelpWriterTest.HandlesHelpText (1 ms)
8: [ RUN ] CommandLineHelpWriterTest.HandlesKnownIssues
8: [ OK ] CommandLineHelpWriterTest.HandlesKnownIssues (1 ms)
8: [----------] 7 tests from CommandLineHelpWriterTest (10 ms total)
8:
8: [----------] 6 tests from CommandLineModuleManagerTest
8: [ RUN ] CommandLineModuleManagerTest.RunsModule
8: [ OK ] CommandLineModuleManagerTest.RunsModule (1 ms)
8: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelp
8: [ OK ] CommandLineModuleManagerTest.RunsModuleHelp (1 ms)
8: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet
8: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet (1 ms)
8: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH
8: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH (1 ms)
8: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule
8: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule (1 ms)
8: [ RUN ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames
8: [ OK ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames (1 ms)
8: [----------] 6 tests from CommandLineModuleManagerTest (6 ms total)
8:
8: [----------] 13 tests from CommandLineParserTest
8: [ RUN ] CommandLineParserTest.HandlesSingleValues
8: [ OK ] CommandLineParserTest.HandlesSingleValues (0 ms)
8: [ RUN ] CommandLineParserTest.HandlesBooleanWithoutArgument
8: [ OK ] CommandLineParserTest.HandlesBooleanWithoutArgument (0 ms)
8: [ RUN ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument
8: [ OK ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument (0 ms)
8: [ RUN ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument
8: [ OK ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument (1 ms)
8: [ RUN ] CommandLineParserTest.HandlesNegativeNumbers
8: [ OK ] CommandLineParserTest.HandlesNegativeNumbers (1 ms)
8: [ RUN ] CommandLineParserTest.HandlesString
8: [ OK ] CommandLineParserTest.HandlesString (0 ms)
8: [ RUN ] CommandLineParserTest.RejectsStringWithMultipleValues
8: [ OK ] CommandLineParserTest.RejectsStringWithMultipleValues (0 ms)
8: [ RUN ] CommandLineParserTest.HandlesDoubleDashOptionPrefix
8: [ OK ] CommandLineParserTest.HandlesDoubleDashOptionPrefix (0 ms)
8: [ RUN ] CommandLineParserTest.HandlesOptionsStartingWithNumbers
8: [ OK ] CommandLineParserTest.HandlesOptionsStartingWithNumbers (1 ms)
8: [ RUN ] CommandLineParserTest.HandlesSkipUnknown
8: [ OK ] CommandLineParserTest.HandlesSkipUnknown (0 ms)
8: [ RUN ] CommandLineParserTest.RejectsPositionalArgumentsByDefault
8: [ OK ] CommandLineParserTest.RejectsPositionalArgumentsByDefault (0 ms)
8: [ RUN ] CommandLineParserTest.CanAllowPositionalArguments
8: [ OK ] CommandLineParserTest.CanAllowPositionalArguments (0 ms)
8: [ RUN ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions
8: [ OK ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions (0 ms)
8: [----------] 13 tests from CommandLineParserTest (3 ms total)
8:
8: [----------] 6 tests from CommandLineProgramContextTest
8: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath
8: [ OK ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath (1 ms)
8: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithRelativePath
8: [ OK ] CommandLineProgramContextTest.FindsBinaryWithRelativePath (0 ms)
8: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromPath
8: [ OK ] CommandLineProgramContextTest.FindsBinaryFromPath (0 ms)
8: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory
8: [ OK ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory (0 ms)
8: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink
8: [ OK ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink (0 ms)
8: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink
8: [ OK ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink (1 ms)
8: [----------] 6 tests from CommandLineProgramContextTest (2 ms total)
8:
8: [----------] 3 tests from OutputNamesTest
8: [ RUN ] OutputNamesTest.CanBeSuffixed
8: [ OK ] OutputNamesTest.CanBeSuffixed (0 ms)
8: [ RUN ] OutputNamesTest.HasSuffixFromNoAppend
8: [ OK ] OutputNamesTest.HasSuffixFromNoAppend (0 ms)
8: [ RUN ] OutputNamesTest.CanHavePartNumberAdded
8: [ OK ] OutputNamesTest.CanHavePartNumberAdded (0 ms)
8: [----------] 3 tests from OutputNamesTest (0 ms total)
8:
8: [----------] 21 tests from ParseCommonArgsTest
8: [ RUN ] ParseCommonArgsTest.ParsesIntegerArgs
8: [ OK ] ParseCommonArgsTest.ParsesIntegerArgs (0 ms)
8: [ RUN ] ParseCommonArgsTest.ParsesInt64Args
8: [ OK ] ParseCommonArgsTest.ParsesInt64Args (0 ms)
8: [ RUN ] ParseCommonArgsTest.ParsesRealArgs
8: [ OK ] ParseCommonArgsTest.ParsesRealArgs (0 ms)
8: [ RUN ] ParseCommonArgsTest.ParsesStringArgs
8: [ OK ] ParseCommonArgsTest.ParsesStringArgs (0 ms)
8: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgs
8: [ OK ] ParseCommonArgsTest.ParsesBooleanArgs (0 ms)
8: [ RUN ] ParseCommonArgsTest.ParsesVectorArgs
8: [ OK ] ParseCommonArgsTest.ParsesVectorArgs (0 ms)
8: [ RUN ] ParseCommonArgsTest.ParsesTimeArgs
8: [ OK ] ParseCommonArgsTest.ParsesTimeArgs (0 ms)
8: [ RUN ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit
8: [ OK ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit (0 ms)
8: [ RUN ] ParseCommonArgsTest.ParsesEnumArgs
8: [ OK ] ParseCommonArgsTest.ParsesEnumArgs (0 ms)
8: [ RUN ] ParseCommonArgsTest.ParsesFileArgs
8: [ OK ] ParseCommonArgsTest.ParsesFileArgs (0 ms)
8: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaults
8: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaults (0 ms)
8: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName
8: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName (1 ms)
8: [ RUN ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension
8: [ OK ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension (0 ms)
8: [ RUN ] ParseCommonArgsTest.HandlesNonExistentInputFiles
8: [ OK ] ParseCommonArgsTest.HandlesNonExistentInputFiles (1 ms)
8: [ RUN ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles
8: [ OK ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles (1 ms)
8: [ RUN ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified
8: [ OK ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified (1 ms)
8: [ RUN ] ParseCommonArgsTest.HandlesCompressedFiles
8: [ OK ] ParseCommonArgsTest.HandlesCompressedFiles (2 ms)
8: [ RUN ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension
8: [ OK ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension (1 ms)
8: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFile
8: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFile (4 ms)
8: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName
8: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName (4 ms)
8: [ RUN ] ParseCommonArgsTest.CanKeepUnknownArgs
8: [ OK ] ParseCommonArgsTest.CanKeepUnknownArgs (0 ms)
8: [----------] 21 tests from ParseCommonArgsTest (19 ms total)
8:
8: [----------] Global test environment tear-down
8: [==========] 59 tests from 7 test cases ran. (54 ms total)
8: [ PASSED ] 59 tests.
8/52 Test #8: CommandLineUnitTests ................ Passed 0.12 sec
test 9
Start 9: DomDecTests
9: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/domdec-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/DomDecTests.xml"
9: Test timeout computed to be: 30
9: [==========] Running 9 tests from 2 test cases.
9: [----------] Global test environment set-up.
9: [----------] 7 tests from HashedMap
9: [ RUN ] HashedMap.InsertsFinds
9: [ OK ] HashedMap.InsertsFinds (0 ms)
9: [ RUN ] HashedMap.NegativeKeysWork
9: [ OK ] HashedMap.NegativeKeysWork (0 ms)
9: [ RUN ] HashedMap.InsertsErases
9: [ OK ] HashedMap.InsertsErases (0 ms)
9: [ RUN ] HashedMap.InsertsOrAssigns
9: [ OK ] HashedMap.InsertsOrAssigns (0 ms)
9: [ RUN ] HashedMap.Clears
9: [ OK ] HashedMap.Clears (0 ms)
9: [ RUN ] HashedMap.LinkedEntries
9: [ OK ] HashedMap.LinkedEntries (0 ms)
9: [ RUN ] HashedMap.ResizesTable
9: [ OK ] HashedMap.ResizesTable (0 ms)
9: [----------] 7 tests from HashedMap (0 ms total)
9:
9: [----------] 2 tests from LocalAtomSetManager
9: [ RUN ] LocalAtomSetManager.CanAddEmptyLocalAtomSet
9: [ OK ] LocalAtomSetManager.CanAddEmptyLocalAtomSet (0 ms)
9: [ RUN ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices
9: [ OK ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices (0 ms)
9: [----------] 2 tests from LocalAtomSetManager (1 ms total)
9:
9: [----------] Global test environment tear-down
9: [==========] 9 tests from 2 test cases ran. (2 ms total)
9: [ PASSED ] 9 tests.
9/52 Test #9: DomDecTests ......................... Passed 0.06 sec
test 10
Start 10: EwaldUnitTests
10: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/ewald-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/EwaldUnitTests.xml"
10: Test timeout computed to be: 30
10: [==========] Running 257 tests from 10 test cases.
10: [----------] Global test environment set-up.
10: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest
10: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0
10: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 (1 ms)
10: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1
10: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 (0 ms)
10: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2
10: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 (0 ms)
10: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3
10: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 (15 ms)
10: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4
10: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 (0 ms)
10: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest (16 ms total)
10:
10: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 (14 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 (14 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 (13 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 (13 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 (14 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 (14 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 (14 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 (14 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 (15 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 (15 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 (16 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 (16 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 (31 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 (14 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 (15 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 (15 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 (15 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 (15 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 (16 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 (15 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 (16 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 (16 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 (17 ms)
10: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23
10: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 (17 ms)
10: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest (388 ms total)
10:
10: [----------] 144 tests from SaneInput/PmeGatherTest
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/0
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/0 (3 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/1
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/1 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/2
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/2 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/3
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/3 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/4
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/4 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/5
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/5 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/6
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/6 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/7
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/7 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/8
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/8 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/9
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/9 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/10
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/10 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/11
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/11 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/12
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/12 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/13
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/13 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/14
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/14 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/15
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/15 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/16
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/16 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/17
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/17 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/18
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/18 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/19
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/19 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/20
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/20 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/21
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/21 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/22
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/22 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/23
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/23 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/24
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/24 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/25
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/25 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/26
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/26 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/27
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/27 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/28
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/28 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/29
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/29 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/30
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/30 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/31
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/31 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/32
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/32 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/33
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/33 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/34
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/34 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/35
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/35 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/36
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/36 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/37
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/37 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/38
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/38 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/39
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/39 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/40
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/40 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/41
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/41 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/42
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/42 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/43
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/43 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/44
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/44 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/45
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/45 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/46
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/46 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/47
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/47 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/48
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/48 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/49
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/49 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/50
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/50 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/51
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/51 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/52
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/52 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/53
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/53 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/54
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/54 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/55
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/55 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/56
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/56 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/57
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/57 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/58
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/58 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/59
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/59 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/60
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/60 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/61
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/61 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/62
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/62 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/63
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/63 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/64
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/64 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/65
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/65 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/66
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/66 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/67
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/67 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/68
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/68 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/69
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/69 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/70
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/70 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/71
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/71 (3 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/72
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/72 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/73
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/73 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/74
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/74 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/75
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/75 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/76
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/76 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/77
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/77 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/78
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/78 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/79
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/79 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/80
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/80 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/81
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/81 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/82
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/82 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/83
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/83 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/84
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/84 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/85
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/85 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/86
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/86 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/87
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/87 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/88
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/88 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/89
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/89 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/90
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/90 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/91
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/91 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/92
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/92 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/93
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/93 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/94
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/94 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/95
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/95 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/96
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/96 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/97
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/97 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/98
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/98 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/99
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/99 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/100
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/100 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/101
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/101 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/102
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/102 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/103
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/103 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/104
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/104 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/105
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/105 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/106
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/106 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/107
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/107 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/108
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/108 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/109
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/109 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/110
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/110 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/111
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/111 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/112
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/112 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/113
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/113 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/114
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/114 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/115
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/115 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/116
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/116 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/117
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/117 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/118
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/118 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/119
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/119 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/120
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/120 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/121
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/121 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/122
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/122 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/123
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/123 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/124
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/124 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/125
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/125 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/126
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/126 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/127
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/127 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/128
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/128 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/129
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/129 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/130
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/130 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/131
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/131 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/132
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/132 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/133
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/133 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/134
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/134 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/135
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/135 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/136
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/136 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/137
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/137 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/138
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/138 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/139
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/139 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/140
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/140 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/141
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/141 (1 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/142
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/142 (2 ms)
10: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/143
10: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/143 (2 ms)
10: [----------] 144 tests from SaneInput/PmeGatherTest (257 ms total)
10:
10: [----------] 16 tests from SaneInput/PmeSolveTest
10: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/0
10: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/0 (8 ms)
10: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/1
10: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/1 (11 ms)
10: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/2
10: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/2 (6 ms)
10: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/3
10: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/3 (11 ms)
10: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/4
10: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/4 (9 ms)
10: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/5
10: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/5 (6 ms)
10: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/6
10: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/6 (3 ms)
10: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/7
10: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/7 (6 ms)
10: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/8
10: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/8 (5 ms)
10: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/9
10: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/9 (10 ms)
10: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/10
10: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/10 (6 ms)
10: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/11
10: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/11 (11 ms)
10: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/12
10: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/12 (4 ms)
10: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/13
10: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/13 (6 ms)
10: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/14
10: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/14 (3 ms)
10: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/15
10: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/15 (7 ms)
10: [----------] 16 tests from SaneInput/PmeSolveTest (116 ms total)
10:
10: [----------] 8 tests from DifferentEwaldCoeffQ/PmeSolveTest
10: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/0
10: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/0 (6 ms)
10: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/1
10: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/1 (6 ms)
10: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/2
10: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/2 (3 ms)
10: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/3
10: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/3 (3 ms)
10: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/4
10: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/4 (6 ms)
10: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/5
10: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/5 (6 ms)
10: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/6
10: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/6 (4 ms)
10: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/7
10: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/7 (4 ms)
10: [----------] 8 tests from DifferentEwaldCoeffQ/PmeSolveTest (39 ms total)
10:
10: [----------] 8 tests from DifferentEwaldCoeffLJ/PmeSolveTest
10: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/0
10: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/0 (11 ms)
10: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/1
10: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/1 (10 ms)
10: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/2
10: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/2 (6 ms)
10: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/3
10: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/3 (6 ms)
10: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/4
10: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/4 (11 ms)
10: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/5
10: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/5 (10 ms)
10: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/6
10: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/6 (6 ms)
10: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/7
10: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/7 (6 ms)
10: [----------] 8 tests from DifferentEwaldCoeffLJ/PmeSolveTest (68 ms total)
10:
10: [----------] 16 tests from DifferentEpsilonR/PmeSolveTest
10: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/0
10: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/0 (6 ms)
10: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/1
10: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/1 (11 ms)
10: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/2
10: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/2 (6 ms)
10: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/3
10: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/3 (10 ms)
10: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/4
10: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/4 (4 ms)
10: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/5
10: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/5 (6 ms)
10: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/6
10: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/6 (4 ms)
10: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/7
10: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/7 (6 ms)
10: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/8
10: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/8 (6 ms)
10: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/9
10: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/9 (11 ms)
10: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/10
10: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/10 (6 ms)
10: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/11
10: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/11 (11 ms)
10: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/12
10: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/12 (4 ms)
10: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/13
10: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/13 (6 ms)
10: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/14
10: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/14 (4 ms)
10: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/15
10: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/15 (6 ms)
10: [----------] 16 tests from DifferentEpsilonR/PmeSolveTest (108 ms total)
10:
10: [----------] 12 tests from SaneInput1/PmeSplineAndSpreadTest
10: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/0
10: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/0 (5 ms)
10: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/1
10: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/1 (11 ms)
10: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/2
10: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/2 (6 ms)
10: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/3
10: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/3 (8 ms)
10: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/4
10: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/4 (8 ms)
10: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/5
10: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/5 (9 ms)
10: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/6
10: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/6 (6 ms)
10: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/7
10: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/7 (6 ms)
10: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/8
10: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/8 (6 ms)
10: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/9
10: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/9 (7 ms)
10: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/10
10: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/10 (8 ms)
10: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/11
10: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/11 (9 ms)
10: [----------] 12 tests from SaneInput1/PmeSplineAndSpreadTest (94 ms total)
10:
10: [----------] 12 tests from SaneInput2/PmeSplineAndSpreadTest
10: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/0
10: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/0 (6 ms)
10: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/1
10: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/1 (7 ms)
10: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/2
10: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/2 (8 ms)
10: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/3
10: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/3 (9 ms)
10: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/4
10: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/4 (10 ms)
10: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/5
10: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/5 (12 ms)
10: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/6
10: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/6 (7 ms)
10: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/7
10: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/7 (7 ms)
10: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/8
10: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/8 (9 ms)
10: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/9
10: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/9 (9 ms)
10: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/10
10: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/10 (12 ms)
10: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/11
10: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/11 (13 ms)
10: [----------] 12 tests from SaneInput2/PmeSplineAndSpreadTest (114 ms total)
10:
10: [----------] 12 tests from SaneInput13/PmeSplineAndSpreadTest
10: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/0
10: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/0 (15 ms)
10: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/1
10: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/1 (16 ms)
10: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/2
10: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/2 (23 ms)
10: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/3
10: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/3 (26 ms)
10: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/4
10: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/4 (34 ms)
10: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/5
10: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/5 (37 ms)
10: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/6
10: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/6 (16 ms)
10: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/7
10: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/7 (17 ms)
10: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/8
10: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/8 (22 ms)
10: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/9
10: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/9 (25 ms)
10: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/10
10: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/10 (30 ms)
10: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/11
10: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/11 (36 ms)
10: [----------] 12 tests from SaneInput13/PmeSplineAndSpreadTest (323 ms total)
10:
10: [----------] Global test environment tear-down
10: [==========] 257 tests from 10 test cases ran. (1628 ms total)
10: [ PASSED ] 257 tests.
10/52 Test #10: EwaldUnitTests ...................... Passed 1.85 sec
test 11
Start 11: FFTUnitTests
11: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/fft-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/FFTUnitTests.xml"
11: Test timeout computed to be: 30
11: [==========] Running 14 tests from 4 test cases.
11: [----------] Global test environment set-up.
11: [----------] 2 tests from ManyFFTTest
11: [ RUN ] ManyFFTTest.Complex1DLength48Multi5Test
11: [ OK ] ManyFFTTest.Complex1DLength48Multi5Test (35 ms)
11: [ RUN ] ManyFFTTest.Real1DLength48Multi5Test
11: [ OK ] ManyFFTTest.Real1DLength48Multi5Test (50 ms)
11: [----------] 2 tests from ManyFFTTest (88 ms total)
11:
11: [----------] 1 test from FFTTest
11: [ RUN ] FFTTest.Real2DLength18_15Test
11: [ OK ] FFTTest.Real2DLength18_15Test (13 ms)
11: [----------] 1 test from FFTTest (14 ms total)
11:
11: [----------] 1 test from FFFTest3D
11: [ RUN ] FFFTest3D.Real5_6_9
11: [ OK ] FFFTest3D.Real5_6_9 (10 ms)
11: [----------] 1 test from FFFTest3D (12 ms total)
11:
11: [----------] 10 tests from 7_8_25_36_60/FFTTest1D
11: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/0
11: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/0 (3 ms)
11: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/1
11: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/1 (2 ms)
11: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/2
11: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/2 (4 ms)
11: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/3
11: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/3 (6 ms)
11: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/4
11: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/4 (7 ms)
11: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/0
11: [ OK ] 7_8_25_36_60/FFTTest1D.Real/0 (2 ms)
11: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/1
11: [ OK ] 7_8_25_36_60/FFTTest1D.Real/1 (2 ms)
11: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/2
11: [ OK ] 7_8_25_36_60/FFTTest1D.Real/2 (3 ms)
11: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/3
11: [ OK ] 7_8_25_36_60/FFTTest1D.Real/3 (22 ms)
11: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/4
11: [ OK ] 7_8_25_36_60/FFTTest1D.Real/4 (33 ms)
11: [----------] 10 tests from 7_8_25_36_60/FFTTest1D (88 ms total)
11:
11: [----------] Global test environment tear-down
11: [==========] 14 tests from 4 test cases ran. (204 ms total)
11: [ PASSED ] 14 tests.
11/52 Test #11: FFTUnitTests ........................ Passed 0.27 sec
test 12
Start 12: GpuUtilsUnitTests
12: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/gpu_utils-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/GpuUtilsUnitTests.xml"
12: Test timeout computed to be: 30
12: [==========] Running 62 tests from 20 test cases.
12: [----------] Global test environment set-up.
12: [----------] 2 tests from ClfftInitializer
12: [ RUN ] ClfftInitializer.SingleInitializationWorks
12: [ OK ] ClfftInitializer.SingleInitializationWorks (0 ms)
12: [ RUN ] ClfftInitializer.TwoInitializationsWork
12: [ OK ] ClfftInitializer.TwoInitializationsWork (0 ms)
12: [----------] 2 tests from ClfftInitializer (0 ms total)
12:
12: [----------] 2 tests from HostAllocatorTest/0, where TypeParam = int
12: [ RUN ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks
12: [ OK ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks (0 ms)
12: [ RUN ] HostAllocatorTest/0.StatefulAllocatorUsesMemory
12: [ OK ] HostAllocatorTest/0.StatefulAllocatorUsesMemory (0 ms)
12: [----------] 2 tests from HostAllocatorTest/0 (0 ms total)
12:
12: [----------] 2 tests from HostAllocatorTest/1, where TypeParam = double
12: [ RUN ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks
12: [ OK ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks (0 ms)
12: [ RUN ] HostAllocatorTest/1.StatefulAllocatorUsesMemory
12: [ OK ] HostAllocatorTest/1.StatefulAllocatorUsesMemory (0 ms)
12: [----------] 2 tests from HostAllocatorTest/1 (0 ms total)
12:
12: [----------] 2 tests from HostAllocatorTest/2, where TypeParam = gmx::BasicVector<double>
12: [ RUN ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks
12: [ OK ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks (0 ms)
12: [ RUN ] HostAllocatorTest/2.StatefulAllocatorUsesMemory
12: [ OK ] HostAllocatorTest/2.StatefulAllocatorUsesMemory (0 ms)
12: [----------] 2 tests from HostAllocatorTest/2 (0 ms total)
12:
12: [----------] 2 tests from HostAllocatorTest/3, where TypeParam = gmx::test::MoveOnly
12: [ RUN ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks
12: [ OK ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks (0 ms)
12: [ RUN ] HostAllocatorTest/3.StatefulAllocatorUsesMemory
12: [ OK ] HostAllocatorTest/3.StatefulAllocatorUsesMemory (0 ms)
12: [----------] 2 tests from HostAllocatorTest/3 (1 ms total)
12:
12: [----------] 3 tests from HostAllocatorTestCopyable/0, where TypeParam = int
12: [ RUN ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks
12: [ OK ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms)
12: [ RUN ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork
12: [ OK ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork (0 ms)
12: [ RUN ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve
12: [ OK ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve (0 ms)
12: [----------] 3 tests from HostAllocatorTestCopyable/0 (0 ms total)
12:
12: [----------] 3 tests from HostAllocatorTestCopyable/1, where TypeParam = double
12: [ RUN ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks
12: [ OK ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms)
12: [ RUN ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork
12: [ OK ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork (0 ms)
12: [ RUN ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve
12: [ OK ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve (0 ms)
12: [----------] 3 tests from HostAllocatorTestCopyable/1 (0 ms total)
12:
12: [----------] 3 tests from HostAllocatorTestCopyable/2, where TypeParam = gmx::BasicVector<double>
12: [ RUN ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks
12: [ OK ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms)
12: [ RUN ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork
12: [ OK ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork (0 ms)
12: [ RUN ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve
12: [ OK ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve (0 ms)
12: [----------] 3 tests from HostAllocatorTestCopyable/2 (0 ms total)
12:
12: [----------] 5 tests from HostAllocatorTestNoMem/0, where TypeParam = int
12: [ RUN ] HostAllocatorTestNoMem/0.CreateVector
12: [ OK ] HostAllocatorTestNoMem/0.CreateVector (0 ms)
12: [ RUN ] HostAllocatorTestNoMem/0.MoveAssignment
12: [ OK ] HostAllocatorTestNoMem/0.MoveAssignment (0 ms)
12: [ RUN ] HostAllocatorTestNoMem/0.MoveConstruction
12: [ OK ] HostAllocatorTestNoMem/0.MoveConstruction (0 ms)
12: [ RUN ] HostAllocatorTestNoMem/0.Swap
12: [ OK ] HostAllocatorTestNoMem/0.Swap (0 ms)
12: [ RUN ] HostAllocatorTestNoMem/0.Comparison
12: [ OK ] HostAllocatorTestNoMem/0.Comparison (0 ms)
12: [----------] 5 tests from HostAllocatorTestNoMem/0 (1 ms total)
12:
12: [----------] 5 tests from HostAllocatorTestNoMem/1, where TypeParam = double
12: [ RUN ] HostAllocatorTestNoMem/1.CreateVector
12: [ OK ] HostAllocatorTestNoMem/1.CreateVector (0 ms)
12: [ RUN ] HostAllocatorTestNoMem/1.MoveAssignment
12: [ OK ] HostAllocatorTestNoMem/1.MoveAssignment (0 ms)
12: [ RUN ] HostAllocatorTestNoMem/1.MoveConstruction
12: [ OK ] HostAllocatorTestNoMem/1.MoveConstruction (0 ms)
12: [ RUN ] HostAllocatorTestNoMem/1.Swap
12: [ OK ] HostAllocatorTestNoMem/1.Swap (0 ms)
12: [ RUN ] HostAllocatorTestNoMem/1.Comparison
12: [ OK ] HostAllocatorTestNoMem/1.Comparison (0 ms)
12: [----------] 5 tests from HostAllocatorTestNoMem/1 (0 ms total)
12:
12: [----------] 5 tests from HostAllocatorTestNoMem/2, where TypeParam = gmx::BasicVector<double>
12: [ RUN ] HostAllocatorTestNoMem/2.CreateVector
12: [ OK ] HostAllocatorTestNoMem/2.CreateVector (0 ms)
12: [ RUN ] HostAllocatorTestNoMem/2.MoveAssignment
12: [ OK ] HostAllocatorTestNoMem/2.MoveAssignment (0 ms)
12: [ RUN ] HostAllocatorTestNoMem/2.MoveConstruction
12: [ OK ] HostAllocatorTestNoMem/2.MoveConstruction (0 ms)
12: [ RUN ] HostAllocatorTestNoMem/2.Swap
12: [ OK ] HostAllocatorTestNoMem/2.Swap (0 ms)
12: [ RUN ] HostAllocatorTestNoMem/2.Comparison
12: [ OK ] HostAllocatorTestNoMem/2.Comparison (0 ms)
12: [----------] 5 tests from HostAllocatorTestNoMem/2 (0 ms total)
12:
12: [----------] 5 tests from HostAllocatorTestNoMem/3, where TypeParam = gmx::test::MoveOnly
12: [ RUN ] HostAllocatorTestNoMem/3.CreateVector
12: [ OK ] HostAllocatorTestNoMem/3.CreateVector (0 ms)
12: [ RUN ] HostAllocatorTestNoMem/3.MoveAssignment
12: [ OK ] HostAllocatorTestNoMem/3.MoveAssignment (0 ms)
12: [ RUN ] HostAllocatorTestNoMem/3.MoveConstruction
12: [ OK ] HostAllocatorTestNoMem/3.MoveConstruction (0 ms)
12: [ RUN ] HostAllocatorTestNoMem/3.Swap
12: [ OK ] HostAllocatorTestNoMem/3.Swap (0 ms)
12: [ RUN ] HostAllocatorTestNoMem/3.Comparison
12: [ OK ] HostAllocatorTestNoMem/3.Comparison (0 ms)
12: [----------] 5 tests from HostAllocatorTestNoMem/3 (0 ms total)
12:
12: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0, where TypeParam = int
12: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyAssignment
12: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyAssignment (0 ms)
12: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstruction
12: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstruction (0 ms)
12: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0 (0 ms total)
12:
12: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1, where TypeParam = double
12: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyAssignment
12: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyAssignment (0 ms)
12: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstruction
12: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstruction (0 ms)
12: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1 (0 ms total)
12:
12: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2, where TypeParam = gmx::BasicVector<double>
12: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyAssignment
12: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyAssignment (0 ms)
12: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstruction
12: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstruction (0 ms)
12: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2 (0 ms total)
12:
12: [----------] 1 test from HostAllocatorUntypedTest
12: [ RUN ] HostAllocatorUntypedTest.Comparison
12: [ OK ] HostAllocatorUntypedTest.Comparison (0 ms)
12: [----------] 1 test from HostAllocatorUntypedTest (0 ms total)
12:
12: [----------] 4 tests from AllocatorTest/0, where TypeParam = gmx::Allocator<double, gmx::HostAllocationPolicy>
12: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment
12: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms)
12: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment
12: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (1 ms)
12: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment
12: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms)
12: [ RUN ] AllocatorTest/0.Move
12: [ OK ] AllocatorTest/0.Move (0 ms)
12: [----------] 4 tests from AllocatorTest/0 (1 ms total)
12:
12: [----------] 4 tests from AllocatorTest/1, where TypeParam = gmx::Allocator<int, gmx::HostAllocationPolicy>
12: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment
12: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms)
12: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment
12: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms)
12: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment
12: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms)
12: [ RUN ] AllocatorTest/1.Move
12: [ OK ] AllocatorTest/1.Move (0 ms)
12: [----------] 4 tests from AllocatorTest/1 (1 ms total)
12:
12: [----------] 4 tests from AllocatorTest/2, where TypeParam = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>
12: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment
12: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms)
12: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment
12: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (1 ms)
12: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment
12: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms)
12: [ RUN ] AllocatorTest/2.Move
12: [ OK ] AllocatorTest/2.Move (0 ms)
12: [----------] 4 tests from AllocatorTest/2 (2 ms total)
12:
12: [----------] 4 tests from AllocatorTest/3, where TypeParam = gmx::Allocator<gmx::test::MoveOnly, gmx::HostAllocationPolicy>
12: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment
12: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms)
12: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment
12: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms)
12: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment
12: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms)
12: [ RUN ] AllocatorTest/3.Move
12: [ OK ] AllocatorTest/3.Move (0 ms)
12: [----------] 4 tests from AllocatorTest/3 (0 ms total)
12:
12: [----------] Global test environment tear-down
12: [==========] 62 tests from 20 test cases ran. (8 ms total)
12: [ PASSED ] 62 tests.
12/52 Test #12: GpuUtilsUnitTests ................... Passed 0.08 sec
test 13
Start 13: HardwareUnitTests
13: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/hardware-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/HardwareUnitTests.xml"
13: Test timeout computed to be: 30
13: [==========] Running 4 tests from 1 test case.
13: [----------] Global test environment set-up.
13: [----------] 4 tests from HardwareTopologyTest
13: [ RUN ] HardwareTopologyTest.Execute
13: [ OK ] HardwareTopologyTest.Execute (33 ms)
13: [ RUN ] HardwareTopologyTest.HwlocExecute
13: [ OK ] HardwareTopologyTest.HwlocExecute (31 ms)
13: [ RUN ] HardwareTopologyTest.ProcessorSelfconsistency
13: [ OK ] HardwareTopologyTest.ProcessorSelfconsistency (31 ms)
13: [ RUN ] HardwareTopologyTest.NumaCacheSelfconsistency
13: [ OK ] HardwareTopologyTest.NumaCacheSelfconsistency (31 ms)
13: [----------] 4 tests from HardwareTopologyTest (129 ms total)
13:
13: [----------] Global test environment tear-down
13: [==========] 4 tests from 1 test case ran. (130 ms total)
13: [ PASSED ] 4 tests.
13/52 Test #13: HardwareUnitTests ................... Passed 0.19 sec
test 14
Start 14: MathUnitTests
14: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/math-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MathUnitTests.xml"
14: Test timeout computed to be: 30
14: [==========] Running 204 tests from 29 test cases.
14: [----------] Global test environment set-up.
14: [----------] 1 test from EmptyArrayRefWithPaddingTest
14: [ RUN ] EmptyArrayRefWithPaddingTest.IsEmpty
14: [ OK ] EmptyArrayRefWithPaddingTest.IsEmpty (0 ms)
14: [----------] 1 test from EmptyArrayRefWithPaddingTest (0 ms total)
14:
14: [----------] 1 test from EmptyConstArrayRefWithPaddingTest
14: [ RUN ] EmptyConstArrayRefWithPaddingTest.IsEmpty
14: [ OK ] EmptyConstArrayRefWithPaddingTest.IsEmpty (0 ms)
14: [----------] 1 test from EmptyConstArrayRefWithPaddingTest (1 ms total)
14:
14: [----------] 2 tests from ArrayRefWithPaddingTest/0, where TypeParam = gmx::ArrayRefWithPadding<int>
14: [ RUN ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks
14: [ OK ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks (0 ms)
14: [ RUN ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks
14: [ OK ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks (0 ms)
14: [----------] 2 tests from ArrayRefWithPaddingTest/0 (0 ms total)
14:
14: [----------] 2 tests from ArrayRefWithPaddingTest/1, where TypeParam = gmx::ArrayRefWithPadding<float>
14: [ RUN ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks
14: [ OK ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks (0 ms)
14: [ RUN ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks
14: [ OK ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks (0 ms)
14: [----------] 2 tests from ArrayRefWithPaddingTest/1 (0 ms total)
14:
14: [----------] 2 tests from ArrayRefWithPaddingTest/2, where TypeParam = gmx::ArrayRefWithPadding<double>
14: [ RUN ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks
14: [ OK ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks (0 ms)
14: [ RUN ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks
14: [ OK ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks (0 ms)
14: [----------] 2 tests from ArrayRefWithPaddingTest/2 (0 ms total)
14:
14: [----------] 8 tests from TranslateAndScaleTest
14: [ RUN ] TranslateAndScaleTest.identityTransformation
14: [ OK ] TranslateAndScaleTest.identityTransformation (1 ms)
14: [ RUN ] TranslateAndScaleTest.translationWithIdentityScaling
14: [ OK ] TranslateAndScaleTest.translationWithIdentityScaling (0 ms)
14: [ RUN ] TranslateAndScaleTest.scalingWithZeroTranslation
14: [ OK ] TranslateAndScaleTest.scalingWithZeroTranslation (0 ms)
14: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivial
14: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivial (0 ms)
14: [ RUN ] TranslateAndScaleTest.scalingIdentity
14: [ OK ] TranslateAndScaleTest.scalingIdentity (0 ms)
14: [ RUN ] TranslateAndScaleTest.scalingNonTrivial
14: [ OK ] TranslateAndScaleTest.scalingNonTrivial (0 ms)
14: [ RUN ] TranslateAndScaleTest.scalingInverseNoZero
14: [ OK ] TranslateAndScaleTest.scalingInverseNoZero (1 ms)
14: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero
14: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero (0 ms)
14: [----------] 8 tests from TranslateAndScaleTest (4 ms total)
14:
14: [----------] 12 tests from DensitySimilarityTest
14: [ RUN ] DensitySimilarityTest.InnerProductIsCorrect
14: [ OK ] DensitySimilarityTest.InnerProductIsCorrect (0 ms)
14: [ RUN ] DensitySimilarityTest.InnerProductGradientIsCorrect
14: [ OK ] DensitySimilarityTest.InnerProductGradientIsCorrect (1 ms)
14: [ RUN ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch
14: [ OK ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch (1 ms)
14: [ RUN ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch
14: [ OK ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch (0 ms)
14: [ RUN ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect
14: [ OK ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect (0 ms)
14: [ RUN ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero
14: [ OK ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero (0 ms)
14: [ RUN ] DensitySimilarityTest.RelativeEntropyIsCorrect
14: [ OK ] DensitySimilarityTest.RelativeEntropyIsCorrect (0 ms)
14: [ RUN ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect
14: [ OK ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect (1 ms)
14: [ RUN ] DensitySimilarityTest.CrossCorrelationIsOne
14: [ OK ] DensitySimilarityTest.CrossCorrelationIsOne (186 ms)
14: [ RUN ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated
14: [ OK ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated (196 ms)
14: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated
14: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated (121 ms)
14: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect
14: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect (1 ms)
14: [----------] 12 tests from DensitySimilarityTest (510 ms total)
14:
14: [----------] 6 tests from StructureSimilarityTest
14: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD
14: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD (0 ms)
14: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho
14: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho (0 ms)
14: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSD
14: [ OK ] StructureSimilarityTest.YieldsCorrectRMSD (0 ms)
14: [ RUN ] StructureSimilarityTest.YieldsCorrectRho
14: [ OK ] StructureSimilarityTest.YieldsCorrectRho (0 ms)
14: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex
14: [ OK ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex (0 ms)
14: [ RUN ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex
14: [ OK ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex (0 ms)
14: [----------] 6 tests from StructureSimilarityTest (2 ms total)
14:
14: [----------] 8 tests from ExponentialMovingAverage
14: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero
14: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero (0 ms)
14: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative
14: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative (0 ms)
14: [ RUN ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue
14: [ OK ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue (0 ms)
14: [ RUN ] ExponentialMovingAverage.YieldsCorrectValue
14: [ OK ] ExponentialMovingAverage.YieldsCorrectValue (0 ms)
14: [ RUN ] ExponentialMovingAverage.SetAverageCorrectly
14: [ OK ] ExponentialMovingAverage.SetAverageCorrectly (0 ms)
14: [ RUN ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing
14: [ OK ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing (0 ms)
14: [ RUN ] ExponentialMovingAverage.InverseLagTimeCorrect
14: [ OK ] ExponentialMovingAverage.InverseLagTimeCorrect (0 ms)
14: [ RUN ] ExponentialMovingAverage.RoundTripAsKeyValueTree
14: [ OK ] ExponentialMovingAverage.RoundTripAsKeyValueTree (0 ms)
14: [----------] 8 tests from ExponentialMovingAverage (2 ms total)
14:
14: [----------] 21 tests from FunctionTest
14: [ RUN ] FunctionTest.StaticLog2
14: [ OK ] FunctionTest.StaticLog2 (0 ms)
14: [ RUN ] FunctionTest.Log2I32Bit
14: [ OK ] FunctionTest.Log2I32Bit (1 ms)
14: [ RUN ] FunctionTest.Log2I64Bit
14: [ OK ] FunctionTest.Log2I64Bit (1 ms)
14: [ RUN ] FunctionTest.GreatestCommonDivisor
14: [ OK ] FunctionTest.GreatestCommonDivisor (0 ms)
14: [ RUN ] FunctionTest.InvsqrtFloat
14: [ OK ] FunctionTest.InvsqrtFloat (0 ms)
14: [ RUN ] FunctionTest.InvsqrtDouble
14: [ OK ] FunctionTest.InvsqrtDouble (1 ms)
14: [ RUN ] FunctionTest.InvsqrtInteger
14: [ OK ] FunctionTest.InvsqrtInteger (0 ms)
14: [ RUN ] FunctionTest.InvcbrtFloat
14: [ OK ] FunctionTest.InvcbrtFloat (0 ms)
14: [ RUN ] FunctionTest.InvcbrtDouble
14: [ OK ] FunctionTest.InvcbrtDouble (1 ms)
14: [ RUN ] FunctionTest.InvcbrtInteger
14: [ OK ] FunctionTest.InvcbrtInteger (0 ms)
14: [ RUN ] FunctionTest.SixthrootFloat
14: [ OK ] FunctionTest.SixthrootFloat (0 ms)
14: [ RUN ] FunctionTest.SixthrootDouble
14: [ OK ] FunctionTest.SixthrootDouble (1 ms)
14: [ RUN ] FunctionTest.SixthrootInteger
14: [ OK ] FunctionTest.SixthrootInteger (0 ms)
14: [ RUN ] FunctionTest.InvsixthrootFloat
14: [ OK ] FunctionTest.InvsixthrootFloat (0 ms)
14: [ RUN ] FunctionTest.InvsixthrootDouble
14: [ OK ] FunctionTest.InvsixthrootDouble (1 ms)
14: [ RUN ] FunctionTest.InvsixthrootInteger
14: [ OK ] FunctionTest.InvsixthrootInteger (0 ms)
14: [ RUN ] FunctionTest.Powers
14: [ OK ] FunctionTest.Powers (0 ms)
14: [ RUN ] FunctionTest.ErfInvFloat
14: [ OK ] FunctionTest.ErfInvFloat (0 ms)
14: [ RUN ] FunctionTest.ErfInvDouble
14: [ OK ] FunctionTest.ErfInvDouble (0 ms)
14: [ RUN ] FunctionTest.ErfAndErfInvAreInversesFloat
14: [ OK ] FunctionTest.ErfAndErfInvAreInversesFloat (0 ms)
14: [ RUN ] FunctionTest.ErfAndErfInvAreInversesDouble
14: [ OK ] FunctionTest.ErfAndErfInvAreInversesDouble (2 ms)
14: [----------] 21 tests from FunctionTest (16 ms total)
14:
14: [----------] 4 tests from GaussianOn1DLattice
14: [ RUN ] GaussianOn1DLattice.sumsCloseToOne
14: [ OK ] GaussianOn1DLattice.sumsCloseToOne (0 ms)
14: [ RUN ] GaussianOn1DLattice.isCorrect
14: [ OK ] GaussianOn1DLattice.isCorrect (0 ms)
14: [ RUN ] GaussianOn1DLattice.complementaryAmplitudesSumToZero
14: [ OK ] GaussianOn1DLattice.complementaryAmplitudesSumToZero (0 ms)
14: [ RUN ] GaussianOn1DLattice.doesNotOverflowForLargeRange
14: [ OK ] GaussianOn1DLattice.doesNotOverflowForLargeRange (0 ms)
14: [----------] 4 tests from GaussianOn1DLattice (2 ms total)
14:
14: [----------] 9 tests from GaussTransformTest
14: [ RUN ] GaussTransformTest.isZeroUponConstruction
14: [ OK ] GaussTransformTest.isZeroUponConstruction (0 ms)
14: [ RUN ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss
14: [ OK ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss (1 ms)
14: [ RUN ] GaussTransformTest.isZeroAfterSettingZero
14: [ OK ] GaussTransformTest.isZeroAfterSettingZero (0 ms)
14: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinX
14: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinX (0 ms)
14: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinY
14: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinY (0 ms)
14: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinZ
14: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinZ (0 ms)
14: [ RUN ] GaussTransformTest.complementaryGaussAddToZero
14: [ OK ] GaussTransformTest.complementaryGaussAddToZero (0 ms)
14: [ RUN ] GaussTransformTest.centerGaussianInCubeHasExpectedValues
14: [ OK ] GaussTransformTest.centerGaussianInCubeHasExpectedValues (0 ms)
14: [ RUN ] GaussTransformTest.view
14: [ OK ] GaussTransformTest.view (0 ms)
14: [----------] 9 tests from GaussTransformTest (3 ms total)
14:
14: [----------] 3 tests from DensityFittingForce
14: [ RUN ] DensityFittingForce.isZeroWhenMatchingDensity
14: [ OK ] DensityFittingForce.isZeroWhenMatchingDensity (0 ms)
14: [ RUN ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections
14: [ OK ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections (0 ms)
14: [ RUN ] DensityFittingForce.pullsTowardsDerivative
14: [ OK ] DensityFittingForce.pullsTowardsDerivative (0 ms)
14: [----------] 3 tests from DensityFittingForce (1 ms total)
14:
14: [----------] 2 tests from InvertMatrixTest
14: [ RUN ] InvertMatrixTest.IdentityIsImpotent
14: [ OK ] InvertMatrixTest.IdentityIsImpotent (0 ms)
14: [ RUN ] InvertMatrixTest.ComputesInverse
14: [ OK ] InvertMatrixTest.ComputesInverse (0 ms)
14: [----------] 2 tests from InvertMatrixTest (0 ms total)
14:
14: [----------] 2 tests from InvertBoxMatrixTest
14: [ RUN ] InvertBoxMatrixTest.IdentityIsImpotent
14: [ OK ] InvertBoxMatrixTest.IdentityIsImpotent (0 ms)
14: [ RUN ] InvertBoxMatrixTest.ComputesInverseInPlace
14: [ OK ] InvertBoxMatrixTest.ComputesInverseInPlace (0 ms)
14: [----------] 2 tests from InvertBoxMatrixTest (0 ms total)
14:
14: [----------] 15 tests from MatrixTest
14: [ RUN ] MatrixTest.canSetFromArray
14: [ OK ] MatrixTest.canSetFromArray (0 ms)
14: [ RUN ] MatrixTest.canSetStaticallyFromList
14: [ OK ] MatrixTest.canSetStaticallyFromList (0 ms)
14: [ RUN ] MatrixTest.canConstructAndFill
14: [ OK ] MatrixTest.canConstructAndFill (0 ms)
14: [ RUN ] MatrixTest.canSetValues
14: [ OK ] MatrixTest.canSetValues (0 ms)
14: [ RUN ] MatrixTest.canCopyAssign
14: [ OK ] MatrixTest.canCopyAssign (0 ms)
14: [ RUN ] MatrixTest.canSwap
14: [ OK ] MatrixTest.canSwap (0 ms)
14: [ RUN ] MatrixTest.staticMultiDimArrayExtent
14: [ OK ] MatrixTest.staticMultiDimArrayExtent (0 ms)
14: [ RUN ] MatrixTest.determinantWorks
14: [ OK ] MatrixTest.determinantWorks (0 ms)
14: [ RUN ] MatrixTest.noninvertableDeterminantIsZero
14: [ OK ] MatrixTest.noninvertableDeterminantIsZero (0 ms)
14: [ RUN ] MatrixTest.determinantOfDiagonalMatrix
14: [ OK ] MatrixTest.determinantOfDiagonalMatrix (0 ms)
14: [ RUN ] MatrixTest.traceWorks
14: [ OK ] MatrixTest.traceWorks (0 ms)
14: [ RUN ] MatrixTest.transposeWorks
14: [ OK ] MatrixTest.transposeWorks (0 ms)
14: [ RUN ] MatrixTest.transposeOfSymmetricMatrix
14: [ OK ] MatrixTest.transposeOfSymmetricMatrix (0 ms)
14: [ RUN ] MatrixTest.canCreateFromLegacyMatrix
14: [ OK ] MatrixTest.canCreateFromLegacyMatrix (0 ms)
14: [ RUN ] MatrixTest.canFillLegacyMatrix
14: [ OK ] MatrixTest.canFillLegacyMatrix (0 ms)
14: [----------] 15 tests from MatrixTest (4 ms total)
14:
14: [----------] 25 tests from MultiDimArrayTest
14: [ RUN ] MultiDimArrayTest.canConstructAndFillStatic
14: [ OK ] MultiDimArrayTest.canConstructAndFillStatic (0 ms)
14: [ RUN ] MultiDimArrayTest.canConstructAndFillDynamic
14: [ OK ] MultiDimArrayTest.canConstructAndFillDynamic (0 ms)
14: [ RUN ] MultiDimArrayTest.canSetValuesInStatic
14: [ OK ] MultiDimArrayTest.canSetValuesInStatic (0 ms)
14: [ RUN ] MultiDimArrayTest.canSetValuesInDynamic
14: [ OK ] MultiDimArrayTest.canSetValuesInDynamic (0 ms)
14: [ RUN ] MultiDimArrayTest.canMoveConstructStatic
14: [ OK ] MultiDimArrayTest.canMoveConstructStatic (0 ms)
14: [ RUN ] MultiDimArrayTest.canMoveConstructDynamic
14: [ OK ] MultiDimArrayTest.canMoveConstructDynamic (0 ms)
14: [ RUN ] MultiDimArrayTest.canMoveAssignStatic
14: [ OK ] MultiDimArrayTest.canMoveAssignStatic (0 ms)
14: [ RUN ] MultiDimArrayTest.canMoveAssignDynamic
14: [ OK ] MultiDimArrayTest.canMoveAssignDynamic (0 ms)
14: [ RUN ] MultiDimArrayTest.canCopyConstructStatic
14: [ OK ] MultiDimArrayTest.canCopyConstructStatic (0 ms)
14: [ RUN ] MultiDimArrayTest.canCopyConstructDynamic
14: [ OK ] MultiDimArrayTest.canCopyConstructDynamic (0 ms)
14: [ RUN ] MultiDimArrayTest.canCopyAssignStatic
14: [ OK ] MultiDimArrayTest.canCopyAssignStatic (0 ms)
14: [ RUN ] MultiDimArrayTest.canCopyAssignDynamic
14: [ OK ] MultiDimArrayTest.canCopyAssignDynamic (0 ms)
14: [ RUN ] MultiDimArrayTest.canSwapStatic
14: [ OK ] MultiDimArrayTest.canSwapStatic (0 ms)
14: [ RUN ] MultiDimArrayTest.canSwapDynamic
14: [ OK ] MultiDimArrayTest.canSwapDynamic (0 ms)
14: [ RUN ] MultiDimArrayTest.staticMultiDimArrayExtent
14: [ OK ] MultiDimArrayTest.staticMultiDimArrayExtent (0 ms)
14: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayExtent
14: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayExtent (0 ms)
14: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent
14: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent (0 ms)
14: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue
14: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue (0 ms)
14: [ RUN ] MultiDimArrayTest.staticMultiDimArrayFromArray
14: [ OK ] MultiDimArrayTest.staticMultiDimArrayFromArray (0 ms)
14: [ RUN ] MultiDimArrayTest.conversionToView
14: [ OK ] MultiDimArrayTest.conversionToView (0 ms)
14: [ RUN ] MultiDimArrayTest.conversionToConstView
14: [ OK ] MultiDimArrayTest.conversionToConstView (0 ms)
14: [ RUN ] MultiDimArrayTest.viewBegin
14: [ OK ] MultiDimArrayTest.viewBegin (0 ms)
14: [ RUN ] MultiDimArrayTest.viewEnd
14: [ OK ] MultiDimArrayTest.viewEnd (0 ms)
14: [ RUN ] MultiDimArrayTest.constViewConstBegin
14: [ OK ] MultiDimArrayTest.constViewConstBegin (0 ms)
14: [ RUN ] MultiDimArrayTest.constViewConstEnd
14: [ OK ] MultiDimArrayTest.constViewConstEnd (0 ms)
14: [----------] 25 tests from MultiDimArrayTest (6 ms total)
14:
14: [----------] 4 tests from MultiDimArrayToMdSpanTest
14: [ RUN ] MultiDimArrayToMdSpanTest.convertsToMdSpan
14: [ OK ] MultiDimArrayToMdSpanTest.convertsToMdSpan (0 ms)
14: [ RUN ] MultiDimArrayToMdSpanTest.constArrayToMdSpan
14: [ OK ] MultiDimArrayToMdSpanTest.constArrayToMdSpan (0 ms)
14: [ RUN ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan
14: [ OK ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan (0 ms)
14: [ RUN ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan
14: [ OK ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan (0 ms)
14: [----------] 4 tests from MultiDimArrayToMdSpanTest (0 ms total)
14:
14: [----------] 4 tests from PaddedVectorTest/0, where TypeParam = std::allocator<int>
14: [ RUN ] PaddedVectorTest/0.ConstructsResizesAndReserves
14: [ OK ] PaddedVectorTest/0.ConstructsResizesAndReserves (0 ms)
14: [ RUN ] PaddedVectorTest/0.CanCopyAssign
14: [ OK ] PaddedVectorTest/0.CanCopyAssign (0 ms)
14: [ RUN ] PaddedVectorTest/0.CanMoveAssign
14: [ OK ] PaddedVectorTest/0.CanMoveAssign (0 ms)
14: [ RUN ] PaddedVectorTest/0.CanSwap
14: [ OK ] PaddedVectorTest/0.CanSwap (0 ms)
14: [----------] 4 tests from PaddedVectorTest/0 (1 ms total)
14:
14: [----------] 4 tests from PaddedVectorTest/1, where TypeParam = std::allocator<float>
14: [ RUN ] PaddedVectorTest/1.ConstructsResizesAndReserves
14: [ OK ] PaddedVectorTest/1.ConstructsResizesAndReserves (0 ms)
14: [ RUN ] PaddedVectorTest/1.CanCopyAssign
14: [ OK ] PaddedVectorTest/1.CanCopyAssign (0 ms)
14: [ RUN ] PaddedVectorTest/1.CanMoveAssign
14: [ OK ] PaddedVectorTest/1.CanMoveAssign (0 ms)
14: [ RUN ] PaddedVectorTest/1.CanSwap
14: [ OK ] PaddedVectorTest/1.CanSwap (0 ms)
14: [----------] 4 tests from PaddedVectorTest/1 (1 ms total)
14:
14: [----------] 4 tests from PaddedVectorTest/2, where TypeParam = std::allocator<double>
14: [ RUN ] PaddedVectorTest/2.ConstructsResizesAndReserves
14: [ OK ] PaddedVectorTest/2.ConstructsResizesAndReserves (0 ms)
14: [ RUN ] PaddedVectorTest/2.CanCopyAssign
14: [ OK ] PaddedVectorTest/2.CanCopyAssign (0 ms)
14: [ RUN ] PaddedVectorTest/2.CanMoveAssign
14: [ OK ] PaddedVectorTest/2.CanMoveAssign (0 ms)
14: [ RUN ] PaddedVectorTest/2.CanSwap
14: [ OK ] PaddedVectorTest/2.CanSwap (0 ms)
14: [----------] 4 tests from PaddedVectorTest/2 (1 ms total)
14:
14: [----------] 4 tests from PaddedVectorTest/3, where TypeParam = std::allocator<gmx::BasicVector<float> >
14: [ RUN ] PaddedVectorTest/3.ConstructsResizesAndReserves
14: [ OK ] PaddedVectorTest/3.ConstructsResizesAndReserves (0 ms)
14: [ RUN ] PaddedVectorTest/3.CanCopyAssign
14: [ OK ] PaddedVectorTest/3.CanCopyAssign (0 ms)
14: [ RUN ] PaddedVectorTest/3.CanMoveAssign
14: [ OK ] PaddedVectorTest/3.CanMoveAssign (0 ms)
14: [ RUN ] PaddedVectorTest/3.CanSwap
14: [ OK ] PaddedVectorTest/3.CanSwap (0 ms)
14: [----------] 4 tests from PaddedVectorTest/3 (1 ms total)
14:
14: [----------] 4 tests from PaddedVectorTest/4, where TypeParam = std::allocator<gmx::BasicVector<double> >
14: [ RUN ] PaddedVectorTest/4.ConstructsResizesAndReserves
14: [ OK ] PaddedVectorTest/4.ConstructsResizesAndReserves (0 ms)
14: [ RUN ] PaddedVectorTest/4.CanCopyAssign
14: [ OK ] PaddedVectorTest/4.CanCopyAssign (0 ms)
14: [ RUN ] PaddedVectorTest/4.CanMoveAssign
14: [ OK ] PaddedVectorTest/4.CanMoveAssign (0 ms)
14: [ RUN ] PaddedVectorTest/4.CanSwap
14: [ OK ] PaddedVectorTest/4.CanSwap (0 ms)
14: [----------] 4 tests from PaddedVectorTest/4 (1 ms total)
14:
14: [----------] 4 tests from PaddedVectorTest/5, where TypeParam = gmx::Allocator<int, gmx::AlignedAllocationPolicy>
14: [ RUN ] PaddedVectorTest/5.ConstructsResizesAndReserves
14: [ OK ] PaddedVectorTest/5.ConstructsResizesAndReserves (0 ms)
14: [ RUN ] PaddedVectorTest/5.CanCopyAssign
14: [ OK ] PaddedVectorTest/5.CanCopyAssign (0 ms)
14: [ RUN ] PaddedVectorTest/5.CanMoveAssign
14: [ OK ] PaddedVectorTest/5.CanMoveAssign (0 ms)
14: [ RUN ] PaddedVectorTest/5.CanSwap
14: [ OK ] PaddedVectorTest/5.CanSwap (0 ms)
14: [----------] 4 tests from PaddedVectorTest/5 (1 ms total)
14:
14: [----------] 4 tests from PaddedVectorTest/6, where TypeParam = gmx::Allocator<float, gmx::AlignedAllocationPolicy>
14: [ RUN ] PaddedVectorTest/6.ConstructsResizesAndReserves
14: [ OK ] PaddedVectorTest/6.ConstructsResizesAndReserves (0 ms)
14: [ RUN ] PaddedVectorTest/6.CanCopyAssign
14: [ OK ] PaddedVectorTest/6.CanCopyAssign (0 ms)
14: [ RUN ] PaddedVectorTest/6.CanMoveAssign
14: [ OK ] PaddedVectorTest/6.CanMoveAssign (0 ms)
14: [ RUN ] PaddedVectorTest/6.CanSwap
14: [ OK ] PaddedVectorTest/6.CanSwap (0 ms)
14: [----------] 4 tests from PaddedVectorTest/6 (1 ms total)
14:
14: [----------] 4 tests from PaddedVectorTest/7, where TypeParam = gmx::Allocator<double, gmx::AlignedAllocationPolicy>
14: [ RUN ] PaddedVectorTest/7.ConstructsResizesAndReserves
14: [ OK ] PaddedVectorTest/7.ConstructsResizesAndReserves (0 ms)
14: [ RUN ] PaddedVectorTest/7.CanCopyAssign
14: [ OK ] PaddedVectorTest/7.CanCopyAssign (0 ms)
14: [ RUN ] PaddedVectorTest/7.CanMoveAssign
14: [ OK ] PaddedVectorTest/7.CanMoveAssign (0 ms)
14: [ RUN ] PaddedVectorTest/7.CanSwap
14: [ OK ] PaddedVectorTest/7.CanSwap (0 ms)
14: [----------] 4 tests from PaddedVectorTest/7 (1 ms total)
14:
14: [----------] 4 tests from PaddedVectorTest/8, where TypeParam = gmx::Allocator<gmx::BasicVector<float>, gmx::AlignedAllocationPolicy>
14: [ RUN ] PaddedVectorTest/8.ConstructsResizesAndReserves
14: [ OK ] PaddedVectorTest/8.ConstructsResizesAndReserves (0 ms)
14: [ RUN ] PaddedVectorTest/8.CanCopyAssign
14: [ OK ] PaddedVectorTest/8.CanCopyAssign (0 ms)
14: [ RUN ] PaddedVectorTest/8.CanMoveAssign
14: [ OK ] PaddedVectorTest/8.CanMoveAssign (0 ms)
14: [ RUN ] PaddedVectorTest/8.CanSwap
14: [ OK ] PaddedVectorTest/8.CanSwap (0 ms)
14: [----------] 4 tests from PaddedVectorTest/8 (1 ms total)
14:
14: [----------] 4 tests from PaddedVectorTest/9, where TypeParam = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>
14: [ RUN ] PaddedVectorTest/9.ConstructsResizesAndReserves
14: [ OK ] PaddedVectorTest/9.ConstructsResizesAndReserves (0 ms)
14: [ RUN ] PaddedVectorTest/9.CanCopyAssign
14: [ OK ] PaddedVectorTest/9.CanCopyAssign (0 ms)
14: [ RUN ] PaddedVectorTest/9.CanMoveAssign
14: [ OK ] PaddedVectorTest/9.CanMoveAssign (0 ms)
14: [ RUN ] PaddedVectorTest/9.CanSwap
14: [ OK ] PaddedVectorTest/9.CanSwap (0 ms)
14: [----------] 4 tests from PaddedVectorTest/9 (1 ms total)
14:
14: [----------] 37 tests from RVecTest
14: [ RUN ] RVecTest.CanBeStoredInVector
14: [ OK ] RVecTest.CanBeStoredInVector (0 ms)
14: [ RUN ] RVecTest.ConvertsImplicitlyFrom_rvec
14: [ OK ] RVecTest.ConvertsImplicitlyFrom_rvec (0 ms)
14: [ RUN ] RVecTest.ConvertsImplicitlyTo_rvec
14: [ OK ] RVecTest.ConvertsImplicitlyTo_rvec (0 ms)
14: [ RUN ] RVecTest.WorksAsMutable_rvec
14: [ OK ] RVecTest.WorksAsMutable_rvec (0 ms)
14: [ RUN ] RVecTest.WorksAs_rvec_Array
14: [ OK ] RVecTest.WorksAs_rvec_Array (0 ms)
14: [ RUN ] RVecTest.CanAddRVecToRvec
14: [ OK ] RVecTest.CanAddRVecToRvec (0 ms)
14: [ RUN ] RVecTest.CanAddAssignRVecToRvec
14: [ OK ] RVecTest.CanAddAssignRVecToRvec (0 ms)
14: [ RUN ] RVecTest.CanSubtractRVecFromRvec
14: [ OK ] RVecTest.CanSubtractRVecFromRvec (0 ms)
14: [ RUN ] RVecTest.CanSubtractAssignRVecFromRvec
14: [ OK ] RVecTest.CanSubtractAssignRVecFromRvec (0 ms)
14: [ RUN ] RVecTest.CanDotProductRVecByRvec
14: [ OK ] RVecTest.CanDotProductRVecByRvec (0 ms)
14: [ RUN ] RVecTest.CanCrossProductRVecByRvec
14: [ OK ] RVecTest.CanCrossProductRVecByRvec (0 ms)
14: [ RUN ] RVecTest.CanDivideRVecInplace
14: [ OK ] RVecTest.CanDivideRVecInplace (0 ms)
14: [ RUN ] RVecTest.CanScaleRVec
14: [ OK ] RVecTest.CanScaleRVec (0 ms)
14: [ RUN ] RVecTest.CanDivideRVec
14: [ OK ] RVecTest.CanDivideRVec (0 ms)
14: [ RUN ] RVecTest.CanDoUnitvFromRVec
14: [ OK ] RVecTest.CanDoUnitvFromRVec (0 ms)
14: [ RUN ] RVecTest.CanSqLengthOfRVec
14: [ OK ] RVecTest.CanSqLengthOfRVec (0 ms)
14: [ RUN ] RVecTest.CanLengthOfRVec
14: [ OK ] RVecTest.CanLengthOfRVec (0 ms)
14: [ RUN ] RVecTest.CanCastToRVec
14: [ OK ] RVecTest.CanCastToRVec (0 ms)
14: [ RUN ] RVecTest.CanCastToDVec
14: [ OK ] RVecTest.CanCastToDVec (0 ms)
14: [ RUN ] RVecTest.CanLeftScalarMultiply
14: [ OK ] RVecTest.CanLeftScalarMultiply (0 ms)
14: [ RUN ] RVecTest.CanRightScalarMultiply
14: [ OK ] RVecTest.CanRightScalarMultiply (0 ms)
14: [ RUN ] RVecTest.CanGetUnitvFromRVec
14: [ OK ] RVecTest.CanGetUnitvFromRVec (0 ms)
14: [ RUN ] RVecTest.CanGetSqLengthOfRVec
14: [ OK ] RVecTest.CanGetSqLengthOfRVec (0 ms)
14: [ RUN ] RVecTest.CanGetLengthOfRVec
14: [ OK ] RVecTest.CanGetLengthOfRVec (0 ms)
14: [ RUN ] RVecTest.CanDoCrossProductOfRVec
14: [ OK ] RVecTest.CanDoCrossProductOfRVec (0 ms)
14: [ RUN ] RVecTest.CanDoDotProductOfRVec
14: [ OK ] RVecTest.CanDoDotProductOfRVec (0 ms)
14: [ RUN ] RVecTest.CanScaleByVector
14: [ OK ] RVecTest.CanScaleByVector (0 ms)
14: [ RUN ] RVecTest.asIVec
14: [ OK ] RVecTest.asIVec (1 ms)
14: [ RUN ] RVecTest.elementWiseMin
14: [ OK ] RVecTest.elementWiseMin (0 ms)
14: [ RUN ] RVecTest.elementWiseMax
14: [ OK ] RVecTest.elementWiseMax (0 ms)
14: [ RUN ] RVecTest.WorksAs_dvec_Reference
14: [ OK ] RVecTest.WorksAs_dvec_Reference (0 ms)
14: [ RUN ] RVecTest.WorksAs_ivec_Reference
14: [ OK ] RVecTest.WorksAs_ivec_Reference (0 ms)
14: [ RUN ] RVecTest.WorksAs_rvec_Reference
14: [ OK ] RVecTest.WorksAs_rvec_Reference (0 ms)
14: [ RUN ] RVecTest.CopyConstructorWorks
14: [ OK ] RVecTest.CopyConstructorWorks (0 ms)
14: [ RUN ] RVecTest.CopyAssignmentWorks
14: [ OK ] RVecTest.CopyAssignmentWorks (0 ms)
14: [ RUN ] RVecTest.MoveConstructorWorks
14: [ OK ] RVecTest.MoveConstructorWorks (0 ms)
14: [ RUN ] RVecTest.MoveAssignmentWorks
14: [ OK ] RVecTest.MoveAssignmentWorks (0 ms)
14: [----------] 37 tests from RVecTest (2 ms total)
14:
14: [----------] Global test environment tear-down
14: [==========] 204 tests from 29 test cases ran. (574 ms total)
14: [ PASSED ] 204 tests.
14/52 Test #14: MathUnitTests ....................... Passed 0.66 sec
test 15
Start 15: MdrunUtilityUnitTests
15: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrunutility-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunUtilityUnitTests.xml"
15: Test timeout computed to be: 30
15: [==========] Running 17 tests from 1 test case.
15: [----------] Global test environment set-up.
15: [----------] 17 tests from ThreadAffinityTest
15: [ RUN ] ThreadAffinityTest.DoesNothingWhenDisabled
15: [ OK ] ThreadAffinityTest.DoesNothingWhenDisabled (0 ms)
15: [ RUN ] ThreadAffinityTest.DoesNothingWhenNotSupported
15: [ OK ] ThreadAffinityTest.DoesNothingWhenNotSupported (0 ms)
15: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads
15: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads (1 ms)
15: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads
15: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads (0 ms)
15: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads
15: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads (1 ms)
15: [ RUN ] ThreadAffinityTest.DoesNothingWithUnknownHardware
15: [ OK ] ThreadAffinityTest.DoesNothingWithUnknownHardware (0 ms)
15: [ RUN ] ThreadAffinityTest.DoesNothingWithTooManyThreads
15: [ OK ] ThreadAffinityTest.DoesNothingWithTooManyThreads (0 ms)
15: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeOffset
15: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeOffset (1 ms)
15: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeStride
15: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeStride (1 ms)
15: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithAuto
15: [ OK ] ThreadAffinityTest.PinsSingleThreadWithAuto (1 ms)
15: [ RUN ] ThreadAffinityTest.PinsSingleThreadWhenForced
15: [ OK ] ThreadAffinityTest.PinsSingleThreadWhenForced (1 ms)
15: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced
15: [ OK ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced (2 ms)
15: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread
15: NOTE: Affinity setting failed.
15: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread (1 ms)
15: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithAuto
15: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithAuto (2 ms)
15: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced
15: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced (1 ms)
15: [ RUN ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads
15: [ OK ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads (1 ms)
15: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing
15: NOTE: Affinity setting for 1/2 threads failed.
15: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing (2 ms)
15: [----------] 17 tests from ThreadAffinityTest (17 ms total)
15:
15: [----------] Global test environment tear-down
15: [==========] 17 tests from 1 test case ran. (17 ms total)
15: [ PASSED ] 17 tests.
15/52 Test #15: MdrunUtilityUnitTests ............... Passed 0.08 sec
test 16
Start 16: MdrunUtilityMpiUnitTests
16: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrunutility-mpi-test "-ntmpi" "4" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunUtilityMpiUnitTests.xml"
16: Test timeout computed to be: 30
16: [==========] Running 13 tests from 2 test cases.
16: [----------] Global test environment set-up.
16: [----------] 6 tests from ThreadAffinityMultiRankTest
16: [ RUN ] ThreadAffinityMultiRankTest.PinsWholeNode
16: [ OK ] ThreadAffinityMultiRankTest.PinsWholeNode (7 ms)
16: [ RUN ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride
16: [ OK ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride (6 ms)
16: [ RUN ] ThreadAffinityMultiRankTest.PinsTwoNodes
16: [ OK ] ThreadAffinityMultiRankTest.PinsTwoNodes (5 ms)
16: [ RUN ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled
16: [ OK ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled (2 ms)
16: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto
16: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto (40 ms)
16: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce
16: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce (3 ms)
16: [----------] 6 tests from ThreadAffinityMultiRankTest (63 ms total)
16:
16: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest
16: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly
16: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly (5 ms)
16: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly
16: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly (4 ms)
16: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster
16: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster (4 ms)
16: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly
16: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly (4 ms)
16: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly
16: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly (3 ms)
16: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly
16: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly (5 ms)
16: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly
16: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly (5 ms)
16: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest (32 ms total)
16:
16: [----------] Global test environment tear-down
16: [==========] 13 tests from 2 test cases ran. (96 ms total)
16: [ PASSED ] 13 tests.
16/52 Test #16: MdrunUtilityMpiUnitTests ............ Passed 0.16 sec
test 17
Start 17: MDSpanTests
17: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdspan-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MDSpanTests.xml"
17: Test timeout computed to be: 30
17: [==========] Running 32 tests from 7 test cases.
17: [----------] Global test environment set-up.
17: [----------] 4 tests from BasicAccessorPolicy
17: [ RUN ] BasicAccessorPolicy.Decay
17: [ OK ] BasicAccessorPolicy.Decay (0 ms)
17: [ RUN ] BasicAccessorPolicy.Access
17: [ OK ] BasicAccessorPolicy.Access (0 ms)
17: [ RUN ] BasicAccessorPolicy.Offset
17: [ OK ] BasicAccessorPolicy.Offset (0 ms)
17: [ RUN ] BasicAccessorPolicy.CopyAccessor
17: [ OK ] BasicAccessorPolicy.CopyAccessor (0 ms)
17: [----------] 4 tests from BasicAccessorPolicy (0 ms total)
17:
17: [----------] 4 tests from ExtentsTest
17: [ RUN ] ExtentsTest.Construction
17: [ OK ] ExtentsTest.Construction (0 ms)
17: [ RUN ] ExtentsTest.PurelyStatic
17: [ OK ] ExtentsTest.PurelyStatic (0 ms)
17: [ RUN ] ExtentsTest.RankNought
17: [ OK ] ExtentsTest.RankNought (0 ms)
17: [ RUN ] ExtentsTest.Assignment
17: [ OK ] ExtentsTest.Assignment (0 ms)
17: [----------] 4 tests from ExtentsTest (0 ms total)
17:
17: [----------] 8 tests from MdSpanExtension
17: [ RUN ] MdSpanExtension.SlicingAllStatic
17: [ OK ] MdSpanExtension.SlicingAllStatic (0 ms)
17: [ RUN ] MdSpanExtension.SlicingDynamic
17: [ OK ] MdSpanExtension.SlicingDynamic (0 ms)
17: [ RUN ] MdSpanExtension.SlicingAllStatic3D
17: [ OK ] MdSpanExtension.SlicingAllStatic3D (0 ms)
17: [ RUN ] MdSpanExtension.SlicingEqualsView3D
17: [ OK ] MdSpanExtension.SlicingEqualsView3D (0 ms)
17: [ RUN ] MdSpanExtension.additionWorks
17: [ OK ] MdSpanExtension.additionWorks (0 ms)
17: [ RUN ] MdSpanExtension.subtractionWorks
17: [ OK ] MdSpanExtension.subtractionWorks (0 ms)
17: [ RUN ] MdSpanExtension.multiplicationWorks
17: [ OK ] MdSpanExtension.multiplicationWorks (0 ms)
17: [ RUN ] MdSpanExtension.divisionWorks
17: [ OK ] MdSpanExtension.divisionWorks (0 ms)
17: [----------] 8 tests from MdSpanExtension (1 ms total)
17:
17: [----------] 3 tests from LayoutTests
17: [ RUN ] LayoutTests.LayoutRightConstruction
17: [ OK ] LayoutTests.LayoutRightConstruction (0 ms)
17: [ RUN ] LayoutTests.LayoutRightProperties
17: [ OK ] LayoutTests.LayoutRightProperties (0 ms)
17: [ RUN ] LayoutTests.LayoutRightOperator
17: [ OK ] LayoutTests.LayoutRightOperator (0 ms)
17: [----------] 3 tests from LayoutTests (0 ms total)
17:
17: [----------] 1 test from MdSpanTest
17: [ RUN ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly
17: [ OK ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly (0 ms)
17: [----------] 1 test from MdSpanTest (0 ms total)
17:
17: [----------] 6 tests from MdSpanTest/0, where TypeParam = gmx::basic_mdspan<int, gmx::extents<5, -1, 3, -1, 1>, gmx::layout_right, gmx::accessor_basic<int> >
17: [ RUN ] MdSpanTest/0.Rank
17: [ OK ] MdSpanTest/0.Rank (0 ms)
17: [ RUN ] MdSpanTest/0.DynamicRank
17: [ OK ] MdSpanTest/0.DynamicRank (0 ms)
17: [ RUN ] MdSpanTest/0.Extents
17: [ OK ] MdSpanTest/0.Extents (0 ms)
17: [ RUN ] MdSpanTest/0.Strides
17: [ OK ] MdSpanTest/0.Strides (0 ms)
17: [ RUN ] MdSpanTest/0.Properties
17: [ OK ] MdSpanTest/0.Properties (0 ms)
17: [ RUN ] MdSpanTest/0.Operator
17: [ OK ] MdSpanTest/0.Operator (0 ms)
17: [----------] 6 tests from MdSpanTest/0 (1 ms total)
17:
17: [----------] 6 tests from MdSpanTest/1, where TypeParam = gmx::basic_mdspan<float, gmx::extents<5, -1, 3, -1, 1>, gmx::layout_right, gmx::accessor_basic<float> >
17: [ RUN ] MdSpanTest/1.Rank
17: [ OK ] MdSpanTest/1.Rank (0 ms)
17: [ RUN ] MdSpanTest/1.DynamicRank
17: [ OK ] MdSpanTest/1.DynamicRank (0 ms)
17: [ RUN ] MdSpanTest/1.Extents
17: [ OK ] MdSpanTest/1.Extents (0 ms)
17: [ RUN ] MdSpanTest/1.Strides
17: [ OK ] MdSpanTest/1.Strides (0 ms)
17: [ RUN ] MdSpanTest/1.Properties
17: [ OK ] MdSpanTest/1.Properties (0 ms)
17: [ RUN ] MdSpanTest/1.Operator
17: [ OK ] MdSpanTest/1.Operator (0 ms)
17: [----------] 6 tests from MdSpanTest/1 (0 ms total)
17:
17: [----------] Global test environment tear-down
17: [==========] 32 tests from 7 test cases ran. (2 ms total)
17: [ PASSED ] 32 tests.
17/52 Test #17: MDSpanTests ......................... Passed 0.07 sec
test 18
Start 18: OnlineHelpUnitTests
18: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/onlinehelp-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/OnlineHelpUnitTests.xml"
18: Test timeout computed to be: 30
18: [==========] Running 22 tests from 4 test cases.
18: [----------] Global test environment set-up.
18: [----------] 6 tests from TextTableFormatterTest
18: [ RUN ] TextTableFormatterTest.HandlesBasicCase
18: [ OK ] TextTableFormatterTest.HandlesBasicCase (2 ms)
18: [ RUN ] TextTableFormatterTest.HandlesEmptyColumnTitles
18: [ OK ] TextTableFormatterTest.HandlesEmptyColumnTitles (0 ms)
18: [ RUN ] TextTableFormatterTest.HandlesIndentation
18: [ OK ] TextTableFormatterTest.HandlesIndentation (1 ms)
18: [ RUN ] TextTableFormatterTest.HandlesOverflowingLines
18: [ OK ] TextTableFormatterTest.HandlesOverflowingLines (0 ms)
18: [ RUN ] TextTableFormatterTest.HandlesLastColumnFolding
18: [ OK ] TextTableFormatterTest.HandlesLastColumnFolding (1 ms)
18: [ RUN ] TextTableFormatterTest.HandlesEmptyColumns
18: [ OK ] TextTableFormatterTest.HandlesEmptyColumns (0 ms)
18: [----------] 6 tests from TextTableFormatterTest (4 ms total)
18:
18: [----------] 3 tests from HelpManagerTest
18: [ RUN ] HelpManagerTest.HandlesRootTopic
18: [ OK ] HelpManagerTest.HandlesRootTopic (1 ms)
18: [ RUN ] HelpManagerTest.HandlesSubTopics
18: [ OK ] HelpManagerTest.HandlesSubTopics (0 ms)
18: [ RUN ] HelpManagerTest.HandlesInvalidTopics
18: [ OK ] HelpManagerTest.HandlesInvalidTopics (1 ms)
18: [----------] 3 tests from HelpManagerTest (2 ms total)
18:
18: [----------] 2 tests from HelpTopicFormattingTest
18: [ RUN ] HelpTopicFormattingTest.FormatsSimpleTopic
18: [ OK ] HelpTopicFormattingTest.FormatsSimpleTopic (1 ms)
18: [ RUN ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics
18: [ OK ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics (1 ms)
18: [----------] 2 tests from HelpTopicFormattingTest (2 ms total)
18:
18: [----------] 11 tests from HelpWriterContextTest
18: [ RUN ] HelpWriterContextTest.FormatsParagraphs
18: [ OK ] HelpWriterContextTest.FormatsParagraphs (0 ms)
18: [ RUN ] HelpWriterContextTest.FormatsRstStyleParagraphs
18: [ OK ] HelpWriterContextTest.FormatsRstStyleParagraphs (1 ms)
18: [ RUN ] HelpWriterContextTest.CleansUpExtraWhitespace
18: [ OK ] HelpWriterContextTest.CleansUpExtraWhitespace (0 ms)
18: [ RUN ] HelpWriterContextTest.FormatsLiteralText
18: [ OK ] HelpWriterContextTest.FormatsLiteralText (1 ms)
18: [ RUN ] HelpWriterContextTest.FormatsLiteralTextAtBeginning
18: [ OK ] HelpWriterContextTest.FormatsLiteralTextAtBeginning (0 ms)
18: [ RUN ] HelpWriterContextTest.FormatsLiteralTextWithIndentation
18: [ OK ] HelpWriterContextTest.FormatsLiteralTextWithIndentation (1 ms)
18: [ RUN ] HelpWriterContextTest.FormatsBulletList
18: [ OK ] HelpWriterContextTest.FormatsBulletList (0 ms)
18: [ RUN ] HelpWriterContextTest.FormatsEnumeratedList
18: [ OK ] HelpWriterContextTest.FormatsEnumeratedList (1 ms)
18: [ RUN ] HelpWriterContextTest.FormatsSimpleTable
18: [ OK ] HelpWriterContextTest.FormatsSimpleTable (1 ms)
18: [ RUN ] HelpWriterContextTest.FormatsGridTable
18: [ OK ] HelpWriterContextTest.FormatsGridTable (0 ms)
18: [ RUN ] HelpWriterContextTest.FormatsTitles
18: [ OK ] HelpWriterContextTest.FormatsTitles (1 ms)
18: [----------] 11 tests from HelpWriterContextTest (6 ms total)
18:
18: [----------] Global test environment tear-down
18: [==========] 22 tests from 4 test cases ran. (14 ms total)
18: [ PASSED ] 22 tests.
18/52 Test #18: OnlineHelpUnitTests ................. Passed 0.08 sec
test 19
Start 19: OptionsUnitTests
19: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/options-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/OptionsUnitTests.xml"
19: Test timeout computed to be: 30
19: [==========] Running 110 tests from 18 test cases.
19: [----------] Global test environment set-up.
19: [----------] 5 tests from AbstractOptionStorageTest
19: [ RUN ] AbstractOptionStorageTest.HandlesSetInFinish
19: [ OK ] AbstractOptionStorageTest.HandlesSetInFinish (1 ms)
19: [ RUN ] AbstractOptionStorageTest.HandlesValueRemoval
19: [ OK ] AbstractOptionStorageTest.HandlesValueRemoval (0 ms)
19: [ RUN ] AbstractOptionStorageTest.HandlesValueAddition
19: [ OK ] AbstractOptionStorageTest.HandlesValueAddition (1 ms)
19: [ RUN ] AbstractOptionStorageTest.HandlesTooManyValueAddition
19: [ OK ] AbstractOptionStorageTest.HandlesTooManyValueAddition (1 ms)
19: [ RUN ] AbstractOptionStorageTest.AllowsEmptyValues
19: [ OK ] AbstractOptionStorageTest.AllowsEmptyValues (0 ms)
19: [----------] 5 tests from AbstractOptionStorageTest (3 ms total)
19:
19: [----------] 8 tests from FileNameOptionTest
19: [ RUN ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension
19: [ OK ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension (1 ms)
19: [ RUN ] FileNameOptionTest.HandlesRequiredOptionWithoutValue
19: [ OK ] FileNameOptionTest.HandlesRequiredOptionWithoutValue (0 ms)
19: [ RUN ] FileNameOptionTest.HandlesOptionalUnsetOption
19: [ OK ] FileNameOptionTest.HandlesOptionalUnsetOption (0 ms)
19: [ RUN ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension
19: [ OK ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension (0 ms)
19: [ RUN ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension
19: [ OK ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension (0 ms)
19: [ RUN ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension
19: [ OK ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension (0 ms)
19: [ RUN ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix
19: [ OK ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix (1 ms)
19: [ RUN ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix
19: [ OK ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix (0 ms)
19: [----------] 8 tests from FileNameOptionTest (2 ms total)
19:
19: [----------] 15 tests from FileNameOptionManagerTest
19: [ RUN ] FileNameOptionManagerTest.AddsMissingExtension
19: [ OK ] FileNameOptionManagerTest.AddsMissingExtension (0 ms)
19: [ RUN ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension
19: [ OK ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension (0 ms)
19: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile
19: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile (1 ms)
19: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile
19: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile (0 ms)
19: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile
19: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile (0 ms)
19: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile
19: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile (0 ms)
19: [ RUN ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified
19: [ OK ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified (0 ms)
19: [ RUN ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified
19: [ OK ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified (0 ms)
19: [ RUN ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified
19: [ OK ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified (0 ms)
19: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile
19: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile (0 ms)
19: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile
19: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile (0 ms)
19: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile
19: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile (0 ms)
19: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile
19: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile (0 ms)
19: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile
19: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile (0 ms)
19: [ RUN ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking
19: [ OK ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking (0 ms)
19: [----------] 15 tests from FileNameOptionManagerTest (2 ms total)
19:
19: [----------] 1 test from OptionsTest
19: [ RUN ] OptionsTest.FailsOnNonsafeStorage
19: [ OK ] OptionsTest.FailsOnNonsafeStorage (0 ms)
19: [----------] 1 test from OptionsTest (0 ms total)
19:
19: [----------] 9 tests from OptionsAssignerTest
19: [ RUN ] OptionsAssignerTest.HandlesMissingRequiredParameter
19: [ OK ] OptionsAssignerTest.HandlesMissingRequiredParameter (0 ms)
19: [ RUN ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue
19: [ OK ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue (0 ms)
19: [ RUN ] OptionsAssignerTest.HandlesInvalidMultipleParameter
19: [ OK ] OptionsAssignerTest.HandlesInvalidMultipleParameter (0 ms)
19: [ RUN ] OptionsAssignerTest.HandlesMultipleParameter
19: [ OK ] OptionsAssignerTest.HandlesMultipleParameter (0 ms)
19: [ RUN ] OptionsAssignerTest.HandlesMissingValue
19: [ OK ] OptionsAssignerTest.HandlesMissingValue (0 ms)
19: [ RUN ] OptionsAssignerTest.HandlesExtraValue
19: [ OK ] OptionsAssignerTest.HandlesExtraValue (0 ms)
19: [ RUN ] OptionsAssignerTest.HandlesGroups
19: [ OK ] OptionsAssignerTest.HandlesGroups (0 ms)
19: [ RUN ] OptionsAssignerTest.HandlesSections
19: [ OK ] OptionsAssignerTest.HandlesSections (0 ms)
19: [ RUN ] OptionsAssignerTest.HandlesMultipleSources
19: [ OK ] OptionsAssignerTest.HandlesMultipleSources (0 ms)
19: [----------] 9 tests from OptionsAssignerTest (1 ms total)
19:
19: [----------] 4 tests from OptionsAssignerBooleanTest
19: [ RUN ] OptionsAssignerBooleanTest.StoresYesValue
19: [ OK ] OptionsAssignerBooleanTest.StoresYesValue (0 ms)
19: [ RUN ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue
19: [ OK ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue (0 ms)
19: [ RUN ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo
19: [ OK ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo (0 ms)
19: [ RUN ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue
19: [ OK ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue (1 ms)
19: [----------] 4 tests from OptionsAssignerBooleanTest (1 ms total)
19:
19: [----------] 13 tests from OptionsAssignerIntegerTest
19: [ RUN ] OptionsAssignerIntegerTest.StoresSingleValue
19: [ OK ] OptionsAssignerIntegerTest.StoresSingleValue (0 ms)
19: [ RUN ] OptionsAssignerIntegerTest.HandlesEmptyValue
19: [ OK ] OptionsAssignerIntegerTest.HandlesEmptyValue (0 ms)
19: [ RUN ] OptionsAssignerIntegerTest.HandlesInvalidValue
19: [ OK ] OptionsAssignerIntegerTest.HandlesInvalidValue (0 ms)
19: [ RUN ] OptionsAssignerIntegerTest.HandlesOverflow
19: [ OK ] OptionsAssignerIntegerTest.HandlesOverflow (0 ms)
19: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValue
19: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValue (0 ms)
19: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet
19: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet (0 ms)
19: [ RUN ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet
19: [ OK ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet (0 ms)
19: [ RUN ] OptionsAssignerIntegerTest.HandlesBothDefaultValues
19: [ OK ] OptionsAssignerIntegerTest.HandlesBothDefaultValues (0 ms)
19: [ RUN ] OptionsAssignerIntegerTest.StoresToVector
19: [ OK ] OptionsAssignerIntegerTest.StoresToVector (0 ms)
19: [ RUN ] OptionsAssignerIntegerTest.HandlesVectors
19: [ OK ] OptionsAssignerIntegerTest.HandlesVectors (0 ms)
19: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue
19: [ OK ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue (0 ms)
19: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue
19: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue (0 ms)
19: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment
19: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment (0 ms)
19: [----------] 13 tests from OptionsAssignerIntegerTest (1 ms total)
19:
19: [----------] 5 tests from OptionsAssignerDoubleTest
19: [ RUN ] OptionsAssignerDoubleTest.StoresSingleValue
19: [ OK ] OptionsAssignerDoubleTest.StoresSingleValue (1 ms)
19: [ RUN ] OptionsAssignerDoubleTest.StoresValueFromFloat
19: [ OK ] OptionsAssignerDoubleTest.StoresValueFromFloat (0 ms)
19: [ RUN ] OptionsAssignerDoubleTest.HandlesEmptyValue
19: [ OK ] OptionsAssignerDoubleTest.HandlesEmptyValue (0 ms)
19: [ RUN ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue
19: [ OK ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue (0 ms)
19: [ RUN ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue
19: [ OK ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue (0 ms)
19: [----------] 5 tests from OptionsAssignerDoubleTest (1 ms total)
19:
19: [----------] 9 tests from OptionsAssignerStringTest
19: [ RUN ] OptionsAssignerStringTest.StoresSingleValue
19: [ OK ] OptionsAssignerStringTest.StoresSingleValue (0 ms)
19: [ RUN ] OptionsAssignerStringTest.HandlesEnumValue
19: [ OK ] OptionsAssignerStringTest.HandlesEnumValue (0 ms)
19: [ RUN ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray
19: [ OK ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray (0 ms)
19: [ RUN ] OptionsAssignerStringTest.HandlesIncorrectEnumValue
19: [ OK ] OptionsAssignerStringTest.HandlesIncorrectEnumValue (0 ms)
19: [ RUN ] OptionsAssignerStringTest.CompletesEnumValue
19: [ OK ] OptionsAssignerStringTest.CompletesEnumValue (0 ms)
19: [ RUN ] OptionsAssignerStringTest.HandlesEnumWithNoValue
19: [ OK ] OptionsAssignerStringTest.HandlesEnumWithNoValue (0 ms)
19: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValue
19: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValue (0 ms)
19: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable
19: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable (0 ms)
19: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector
19: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector (0 ms)
19: [----------] 9 tests from OptionsAssignerStringTest (1 ms total)
19:
19: [----------] 6 tests from OptionsAssignerEnumTest
19: [ RUN ] OptionsAssignerEnumTest.StoresSingleValue
19: [ OK ] OptionsAssignerEnumTest.StoresSingleValue (0 ms)
19: [ RUN ] OptionsAssignerEnumTest.StoresVectorValues
19: [ OK ] OptionsAssignerEnumTest.StoresVectorValues (0 ms)
19: [ RUN ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange
19: [ OK ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange (0 ms)
19: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValue
19: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValue (0 ms)
19: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable
19: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable (0 ms)
19: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector
19: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector (0 ms)
19: [----------] 6 tests from OptionsAssignerEnumTest (0 ms total)
19:
19: [----------] 8 tests from RepeatingOptionSectionTest
19: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstance
19: [ OK ] RepeatingOptionSectionTest.HandlesNoInstance (0 ms)
19: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption
19: [ OK ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption (1 ms)
19: [ RUN ] RepeatingOptionSectionTest.HandlesSingleInstance
19: [ OK ] RepeatingOptionSectionTest.HandlesSingleInstance (0 ms)
19: [ RUN ] RepeatingOptionSectionTest.HandlesDefaultValue
19: [ OK ] RepeatingOptionSectionTest.HandlesDefaultValue (0 ms)
19: [ RUN ] RepeatingOptionSectionTest.HandlesTwoInstances
19: [ OK ] RepeatingOptionSectionTest.HandlesTwoInstances (0 ms)
19: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault
19: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault (0 ms)
19: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault
19: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault (0 ms)
19: [ RUN ] RepeatingOptionSectionTest.HandlesNestedSections
19: [ OK ] RepeatingOptionSectionTest.HandlesNestedSections (0 ms)
19: [----------] 8 tests from RepeatingOptionSectionTest (1 ms total)
19:
19: [----------] 1 test from TimeUnitManagerTest
19: [ RUN ] TimeUnitManagerTest.BasicOperations
19: [ OK ] TimeUnitManagerTest.BasicOperations (0 ms)
19: [----------] 1 test from TimeUnitManagerTest (0 ms total)
19:
19: [----------] 4 tests from TimeUnitBehaviorTest
19: [ RUN ] TimeUnitBehaviorTest.ScalesAssignedOptionValue
19: [ OK ] TimeUnitBehaviorTest.ScalesAssignedOptionValue (0 ms)
19: [ RUN ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues
19: [ OK ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues (0 ms)
19: [ RUN ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources
19: [ OK ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources (0 ms)
19: [ RUN ] TimeUnitBehaviorTest.TimeUnitOptionWorks
19: [ OK ] TimeUnitBehaviorTest.TimeUnitOptionWorks (0 ms)
19: [----------] 4 tests from TimeUnitBehaviorTest (1 ms total)
19:
19: [----------] 2 tests from TreeValueSupportAssignTest
19: [ RUN ] TreeValueSupportAssignTest.AssignsFromTree
19: [ OK ] TreeValueSupportAssignTest.AssignsFromTree (0 ms)
19: [ RUN ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays
19: [ OK ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays (0 ms)
19: [----------] 2 tests from TreeValueSupportAssignTest (0 ms total)
19:
19: [----------] 1 test from TreeValueSupportAssignErrorTest
19: [ RUN ] TreeValueSupportAssignErrorTest.HandlesInvalidValue
19: [ OK ] TreeValueSupportAssignErrorTest.HandlesInvalidValue (0 ms)
19: [----------] 1 test from TreeValueSupportAssignErrorTest (1 ms total)
19:
19: [----------] 5 tests from TreeValueSupportCheckTest
19: [ RUN ] TreeValueSupportCheckTest.HandlesEmpty
19: [ OK ] TreeValueSupportCheckTest.HandlesEmpty (0 ms)
19: [ RUN ] TreeValueSupportCheckTest.HandlesMatchingTree
19: [ OK ] TreeValueSupportCheckTest.HandlesMatchingTree (0 ms)
19: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree1
19: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree1 (0 ms)
19: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree2
19: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree2 (0 ms)
19: [ RUN ] TreeValueSupportCheckTest.DetectsExtraValue
19: [ OK ] TreeValueSupportCheckTest.DetectsExtraValue (0 ms)
19: [----------] 5 tests from TreeValueSupportCheckTest (0 ms total)
19:
19: [----------] 6 tests from TreeValueSupportAdjustTest
19: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultValues
19: [ OK ] TreeValueSupportAdjustTest.FillsDefaultValues (1 ms)
19: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultVectorValues
19: [ OK ] TreeValueSupportAdjustTest.FillsDefaultVectorValues (0 ms)
19: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultObjectValues
19: [ OK ] TreeValueSupportAdjustTest.FillsDefaultObjectValues (1 ms)
19: [ RUN ] TreeValueSupportAdjustTest.NormalizesValues
19: [ OK ] TreeValueSupportAdjustTest.NormalizesValues (0 ms)
19: [ RUN ] TreeValueSupportAdjustTest.MergesDefaultValues
19: [ OK ] TreeValueSupportAdjustTest.MergesDefaultValues (0 ms)
19: [ RUN ] TreeValueSupportAdjustTest.OrdersValues
19: [ OK ] TreeValueSupportAdjustTest.OrdersValues (1 ms)
19: [----------] 6 tests from TreeValueSupportAdjustTest (3 ms total)
19:
19: [----------] 8 tests from TreeValueSupportTest
19: [ RUN ] TreeValueSupportTest.SupportsBooleanOption
19: [ OK ] TreeValueSupportTest.SupportsBooleanOption (0 ms)
19: [ RUN ] TreeValueSupportTest.SupportsIntegerOption
19: [ OK ] TreeValueSupportTest.SupportsIntegerOption (0 ms)
19: [ RUN ] TreeValueSupportTest.SupportsInt64Option
19: [ OK ] TreeValueSupportTest.SupportsInt64Option (1 ms)
19: [ RUN ] TreeValueSupportTest.SupportsStringOption
19: [ OK ] TreeValueSupportTest.SupportsStringOption (0 ms)
19: [ RUN ] TreeValueSupportTest.SupportsFloatOption
19: [ OK ] TreeValueSupportTest.SupportsFloatOption (1 ms)
19: [ RUN ] TreeValueSupportTest.SupportsDoubleOption
19: [ OK ] TreeValueSupportTest.SupportsDoubleOption (1 ms)
19: [ RUN ] TreeValueSupportTest.SupportsEnumIntOption
19: [ OK ] TreeValueSupportTest.SupportsEnumIntOption (0 ms)
19: [ RUN ] TreeValueSupportTest.SupportsEnumOption
19: [ OK ] TreeValueSupportTest.SupportsEnumOption (1 ms)
19: [----------] 8 tests from TreeValueSupportTest (5 ms total)
19:
19: [----------] Global test environment tear-down
19: [==========] 110 tests from 18 test cases ran. (24 ms total)
19: [ PASSED ] 110 tests.
19/52 Test #19: OptionsUnitTests .................... Passed 0.10 sec
test 20
Start 20: PbcutilUnitTest
20: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/pbcutil-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/PbcutilUnitTest.xml"
20: Test timeout computed to be: 30
20: [==========] Running 3 tests from 2 test cases.
20: [----------] Global test environment set-up.
20: [----------] 1 test from PbcTest
20: [ RUN ] PbcTest.CalcShiftsWorks
20: [ OK ] PbcTest.CalcShiftsWorks (3 ms)
20: [----------] 1 test from PbcTest (4 ms total)
20:
20: [----------] 2 tests from PbcEnumsTest
20: [ RUN ] PbcEnumsTest.CenteringTypeNamesAreCorrect
20: [ OK ] PbcEnumsTest.CenteringTypeNamesAreCorrect (0 ms)
20: [ RUN ] PbcEnumsTest.UnitCellTypeNamesAreCorrect
20: [ OK ] PbcEnumsTest.UnitCellTypeNamesAreCorrect (0 ms)
20: [----------] 2 tests from PbcEnumsTest (0 ms total)
20:
20: [----------] Global test environment tear-down
20: [==========] 3 tests from 2 test cases ran. (4 ms total)
20: [ PASSED ] 3 tests.
20/52 Test #20: PbcutilUnitTest ..................... Passed 0.07 sec
test 21
Start 21: RandomUnitTests
21: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/random-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/RandomUnitTests.xml"
21: Test timeout computed to be: 30
21: [==========] Running 44 tests from 10 test cases.
21: [----------] Global test environment set-up.
21: [----------] 4 tests from ExponentialDistributionTest
21: [ RUN ] ExponentialDistributionTest.Output
21: [ OK ] ExponentialDistributionTest.Output (1 ms)
21: [ RUN ] ExponentialDistributionTest.Logical
21: [ OK ] ExponentialDistributionTest.Logical (0 ms)
21: [ RUN ] ExponentialDistributionTest.Reset
21: [ OK ] ExponentialDistributionTest.Reset (0 ms)
21: [ RUN ] ExponentialDistributionTest.AltParam
21: [ OK ] ExponentialDistributionTest.AltParam (0 ms)
21: [----------] 4 tests from ExponentialDistributionTest (1 ms total)
21:
21: [----------] 4 tests from GammaDistributionTest
21: [ RUN ] GammaDistributionTest.Output
21: [ OK ] GammaDistributionTest.Output (1 ms)
21: [ RUN ] GammaDistributionTest.Logical
21: [ OK ] GammaDistributionTest.Logical (0 ms)
21: [ RUN ] GammaDistributionTest.Reset
21: [ OK ] GammaDistributionTest.Reset (0 ms)
21: [ RUN ] GammaDistributionTest.AltParam
21: [ OK ] GammaDistributionTest.AltParam (0 ms)
21: [----------] 4 tests from GammaDistributionTest (1 ms total)
21:
21: [----------] 4 tests from NormalDistributionTest
21: [ RUN ] NormalDistributionTest.Output
21: [ OK ] NormalDistributionTest.Output (1 ms)
21: [ RUN ] NormalDistributionTest.Logical
21: [ OK ] NormalDistributionTest.Logical (0 ms)
21: [ RUN ] NormalDistributionTest.Reset
21: [ OK ] NormalDistributionTest.Reset (0 ms)
21: [ RUN ] NormalDistributionTest.AltParam
21: [ OK ] NormalDistributionTest.AltParam (0 ms)
21: [----------] 4 tests from NormalDistributionTest (1 ms total)
21:
21: [----------] 1 test from SeedTest
21: [ RUN ] SeedTest.makeRandomSeed
21: [ OK ] SeedTest.makeRandomSeed (0 ms)
21: [----------] 1 test from SeedTest (0 ms total)
21:
21: [----------] 6 tests from TabulatedNormalDistributionTest
21: [ RUN ] TabulatedNormalDistributionTest.Output14
21: [ OK ] TabulatedNormalDistributionTest.Output14 (1 ms)
21: [ RUN ] TabulatedNormalDistributionTest.Output16
21: [ OK ] TabulatedNormalDistributionTest.Output16 (0 ms)
21: [ RUN ] TabulatedNormalDistributionTest.OutputDouble14
21: [ OK ] TabulatedNormalDistributionTest.OutputDouble14 (1 ms)
21: [ RUN ] TabulatedNormalDistributionTest.Logical
21: [ OK ] TabulatedNormalDistributionTest.Logical (0 ms)
21: [ RUN ] TabulatedNormalDistributionTest.Reset
21: [ OK ] TabulatedNormalDistributionTest.Reset (0 ms)
21: [ RUN ] TabulatedNormalDistributionTest.AltParam
21: [ OK ] TabulatedNormalDistributionTest.AltParam (0 ms)
21: [----------] 6 tests from TabulatedNormalDistributionTest (2 ms total)
21:
21: [----------] 1 test from TabulatedNormalDistributionTableTest
21: [ RUN ] TabulatedNormalDistributionTableTest.HasValidProperties
21: [ OK ] TabulatedNormalDistributionTableTest.HasValidProperties (9 ms)
21: [----------] 1 test from TabulatedNormalDistributionTableTest (9 ms total)
21:
21: [----------] 6 tests from ThreeFry2x64Test
21: [ RUN ] ThreeFry2x64Test.Logical
21: [ OK ] ThreeFry2x64Test.Logical (0 ms)
21: [ RUN ] ThreeFry2x64Test.InternalCounterSequence
21: [ OK ] ThreeFry2x64Test.InternalCounterSequence (0 ms)
21: [ RUN ] ThreeFry2x64Test.Reseed
21: [ OK ] ThreeFry2x64Test.Reseed (0 ms)
21: [ RUN ] ThreeFry2x64Test.Discard
21: [ OK ] ThreeFry2x64Test.Discard (0 ms)
21: [ RUN ] ThreeFry2x64Test.InvalidCounter
21: [ OK ] ThreeFry2x64Test.InvalidCounter (0 ms)
21: [ RUN ] ThreeFry2x64Test.ExhaustInternalCounter
21: [ OK ] ThreeFry2x64Test.ExhaustInternalCounter (0 ms)
21: [----------] 6 tests from ThreeFry2x64Test (1 ms total)
21:
21: [----------] 4 tests from UniformIntDistributionTest
21: [ RUN ] UniformIntDistributionTest.Output
21: [ OK ] UniformIntDistributionTest.Output (1 ms)
21: [ RUN ] UniformIntDistributionTest.Logical
21: [ OK ] UniformIntDistributionTest.Logical (0 ms)
21: [ RUN ] UniformIntDistributionTest.Reset
21: [ OK ] UniformIntDistributionTest.Reset (0 ms)
21: [ RUN ] UniformIntDistributionTest.AltParam
21: [ OK ] UniformIntDistributionTest.AltParam (0 ms)
21: [----------] 4 tests from UniformIntDistributionTest (1 ms total)
21:
21: [----------] 5 tests from UniformRealDistributionTest
21: [ RUN ] UniformRealDistributionTest.GenerateCanonical
21: [ OK ] UniformRealDistributionTest.GenerateCanonical (0 ms)
21: [ RUN ] UniformRealDistributionTest.Output
21: [ OK ] UniformRealDistributionTest.Output (1 ms)
21: [ RUN ] UniformRealDistributionTest.Logical
21: [ OK ] UniformRealDistributionTest.Logical (0 ms)
21: [ RUN ] UniformRealDistributionTest.Reset
21: [ OK ] UniformRealDistributionTest.Reset (0 ms)
21: [ RUN ] UniformRealDistributionTest.AltParam
21: [ OK ] UniformRealDistributionTest.AltParam (0 ms)
21: [----------] 5 tests from UniformRealDistributionTest (1 ms total)
21:
21: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test
21: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/0
21: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/0 (0 ms)
21: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/1
21: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/1 (1 ms)
21: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/2
21: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/2 (0 ms)
21: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/0
21: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 (0 ms)
21: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/1
21: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 (0 ms)
21: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/2
21: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 (0 ms)
21: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0
21: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 (1 ms)
21: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1
21: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 (0 ms)
21: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2
21: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 (0 ms)
21: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test (3 ms total)
21:
21: [----------] Global test environment tear-down
21: [==========] 44 tests from 10 test cases ran. (20 ms total)
21: [ PASSED ] 44 tests.
21/52 Test #21: RandomUnitTests ..................... Passed 0.12 sec
test 22
Start 22: RestraintTests
22: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/restraintpotential-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/RestraintTests.xml"
22: Test timeout computed to be: 30
22: [==========] Running 1 test from 1 test case.
22: [----------] Global test environment set-up.
22: [----------] 1 test from RestraintManager
22: [ RUN ] RestraintManager.restraintList
22: [ OK ] RestraintManager.restraintList (0 ms)
22: [----------] 1 test from RestraintManager (1 ms total)
22:
22: [----------] Global test environment tear-down
22: [==========] 1 test from 1 test case ran. (1 ms total)
22: [ PASSED ] 1 test.
22/52 Test #22: RestraintTests ...................... Passed 0.06 sec
test 23
Start 23: TableUnitTests
23: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/table-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/TableUnitTests.xml"
23: Test timeout computed to be: 30
23: [==========] Running 16 tests from 2 test cases.
23: [----------] Global test environment set-up.
23: [----------] 8 tests from SplineTableTest/0, where TypeParam = gmx::QuadraticSplineTable
23: [ RUN ] SplineTableTest/0.HandlesIncorrectInput
23: [ OK ] SplineTableTest/0.HandlesIncorrectInput (7 ms)
23: [ RUN ] SplineTableTest/0.Sinc
23: [ OK ] SplineTableTest/0.Sinc (5 ms)
23: [ RUN ] SplineTableTest/0.LJ12
23: [ OK ] SplineTableTest/0.LJ12 (90 ms)
23: [ RUN ] SplineTableTest/0.PmeCorrection
23: [ OK ] SplineTableTest/0.PmeCorrection (7 ms)
23: [ RUN ] SplineTableTest/0.HandlesIncorrectNumericalInput
23: [ OK ] SplineTableTest/0.HandlesIncorrectNumericalInput (2 ms)
23: [ RUN ] SplineTableTest/0.NumericalInputPmeCorr
23: [ OK ] SplineTableTest/0.NumericalInputPmeCorr (6 ms)
23: [ RUN ] SplineTableTest/0.TwoFunctions
23: [ OK ] SplineTableTest/0.TwoFunctions (181 ms)
23: [ RUN ] SplineTableTest/0.ThreeFunctions
23: [ OK ] SplineTableTest/0.ThreeFunctions (218 ms)
23: [----------] 8 tests from SplineTableTest/0 (516 ms total)
23:
23: [----------] 8 tests from SplineTableTest/1, where TypeParam = gmx::CubicSplineTable
23: [ RUN ] SplineTableTest/1.HandlesIncorrectInput
23: [ OK ] SplineTableTest/1.HandlesIncorrectInput (7 ms)
23: [ RUN ] SplineTableTest/1.Sinc
23: [ OK ] SplineTableTest/1.Sinc (10 ms)
23: [ RUN ] SplineTableTest/1.LJ12
23: [ OK ] SplineTableTest/1.LJ12 (227 ms)
23: [ RUN ] SplineTableTest/1.PmeCorrection
23: [ OK ] SplineTableTest/1.PmeCorrection (8 ms)
23: [ RUN ] SplineTableTest/1.HandlesIncorrectNumericalInput
23: [ OK ] SplineTableTest/1.HandlesIncorrectNumericalInput (2 ms)
23: [ RUN ] SplineTableTest/1.NumericalInputPmeCorr
23: [ OK ] SplineTableTest/1.NumericalInputPmeCorr (5 ms)
23: [ RUN ] SplineTableTest/1.TwoFunctions
23: [ OK ] SplineTableTest/1.TwoFunctions (454 ms)
23: [ RUN ] SplineTableTest/1.ThreeFunctions
23: [ OK ] SplineTableTest/1.ThreeFunctions (544 ms)
23: [----------] 8 tests from SplineTableTest/1 (1257 ms total)
23:
23: [----------] Global test environment tear-down
23: [==========] 16 tests from 2 test cases ran. (1773 ms total)
23: [ PASSED ] 16 tests.
23/52 Test #23: TableUnitTests ...................... Passed 1.84 sec
test 24
Start 24: TaskAssignmentUnitTests
24: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/taskassignment-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/TaskAssignmentUnitTests.xml"
24: Test timeout computed to be: 30
24: [==========] Running 3 tests from 2 test cases.
24: [----------] Global test environment set-up.
24: [----------] 2 tests from UserTaskAssignmentStringHandlingTest
24: [ RUN ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork
24: [ OK ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork (2 ms)
24: [ RUN ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid
24: [ OK ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid (0 ms)
24: [----------] 2 tests from UserTaskAssignmentStringHandlingTest (2 ms total)
24:
24: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest
24: [ RUN ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow
24: [ OK ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow (2 ms)
24: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest (2 ms total)
24:
24: [----------] Global test environment tear-down
24: [==========] 3 tests from 2 test cases ran. (4 ms total)
24: [ PASSED ] 3 tests.
24/52 Test #24: TaskAssignmentUnitTests ............. Passed 0.07 sec
test 25
Start 25: TopologyTest
25: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/topology-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/TopologyTest.xml"
25: Test timeout computed to be: 30
25: [==========] Running 11 tests from 3 test cases.
25: [----------] Global test environment set-up.
25: [----------] 3 tests from ExclusionBlockTest
25: [ RUN ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks
25: [ OK ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks (0 ms)
25: [ RUN ] ExclusionBlockTest.ConvertExclusionBlockToBlocka
25: [ OK ] ExclusionBlockTest.ConvertExclusionBlockToBlocka (0 ms)
25: [ RUN ] ExclusionBlockTest.MergeExclusions
25: [ OK ] ExclusionBlockTest.MergeExclusions (0 ms)
25: [----------] 3 tests from ExclusionBlockTest (0 ms total)
25:
25: [----------] 2 tests from MtopTest
25: [ RUN ] MtopTest.RangeBasedLoop
25: [ OK ] MtopTest.RangeBasedLoop (1 ms)
25: [ RUN ] MtopTest.Operators
25: [ OK ] MtopTest.Operators (0 ms)
25: [----------] 2 tests from MtopTest (1 ms total)
25:
25: [----------] 6 tests from SymtabTest
25: [ RUN ] SymtabTest.EmptyOnOpen
25: [ OK ] SymtabTest.EmptyOnOpen (0 ms)
25: [ RUN ] SymtabTest.AddSingleEntry
25: [ OK ] SymtabTest.AddSingleEntry (0 ms)
25: [ RUN ] SymtabTest.AddTwoDistinctEntries
25: [ OK ] SymtabTest.AddTwoDistinctEntries (0 ms)
25: [ RUN ] SymtabTest.TryToAddDuplicates
25: [ OK ] SymtabTest.TryToAddDuplicates (0 ms)
25: [ RUN ] SymtabTest.AddLargeNumberOfEntries
25: [ OK ] SymtabTest.AddLargeNumberOfEntries (0 ms)
25: [ RUN ] SymtabTest.NoDuplicatesInLargeTable
25: [ OK ] SymtabTest.NoDuplicatesInLargeTable (1 ms)
25: [----------] 6 tests from SymtabTest (2 ms total)
25:
25: [----------] Global test environment tear-down
25: [==========] 11 tests from 3 test cases ran. (3 ms total)
25: [ PASSED ] 11 tests.
25/52 Test #25: TopologyTest ........................ Passed 0.07 sec
test 26
Start 26: PullTest
26: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/pull-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/PullTest.xml"
26: Test timeout computed to be: 30
26: [==========] Running 5 tests from 1 test case.
26: [----------] Global test environment set-up.
26: [----------] 5 tests from PullTest
26: [ RUN ] PullTest.MaxPullDistanceXyzScrewBox
26: [ OK ] PullTest.MaxPullDistanceXyzScrewBox (1 ms)
26: [ RUN ] PullTest.MaxPullDistanceXyzCubicBox
26: [ OK ] PullTest.MaxPullDistanceXyzCubicBox (0 ms)
26: [ RUN ] PullTest.MaxPullDistanceXyzTricBox
26: [ OK ] PullTest.MaxPullDistanceXyzTricBox (0 ms)
26: [ RUN ] PullTest.MaxPullDistanceXyzLongBox
26: [ OK ] PullTest.MaxPullDistanceXyzLongBox (0 ms)
26: [ RUN ] PullTest.MaxPullDistanceXySkewedBox
26: [ OK ] PullTest.MaxPullDistanceXySkewedBox (0 ms)
26: [----------] 5 tests from PullTest (1 ms total)
26:
26: [----------] Global test environment tear-down
26: [==========] 5 tests from 1 test case ran. (1 ms total)
26: [ PASSED ] 5 tests.
26/52 Test #26: PullTest ............................ Passed 0.06 sec
test 27
Start 27: AwhTest
27: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/awh-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/AwhTest.xml"
27: Test timeout computed to be: 30
27: [==========] Running 12 tests from 4 test cases.
27: [----------] Global test environment set-up.
27: [----------] 1 test from BiasTest
27: [ RUN ] BiasTest.DetectsCovering
27: [ OK ] BiasTest.DetectsCovering (4 ms)
27: [----------] 1 test from BiasTest (4 ms total)
27:
27: [----------] 1 test from gridTest
27: [ RUN ] gridTest.neighborhood
27: [ OK ] gridTest.neighborhood (9 ms)
27: [----------] 1 test from gridTest (9 ms total)
27:
27: [----------] 8 tests from WithParameters/BiasTest
27: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/0
27: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/0 (3 ms)
27: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/1
27: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/1 (2 ms)
27: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/2
27: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/2 (2 ms)
27: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/3
27: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/3 (2 ms)
27: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/4
27: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/4 (2 ms)
27: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/5
27: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/5 (2 ms)
27: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/6
27: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/6 (2 ms)
27: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/7
27: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/7 (2 ms)
27: [----------] 8 tests from WithParameters/BiasTest (19 ms total)
27:
27: [----------] 2 tests from WithParameters/BiasStateTest
27: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/0
27: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/0 (1 ms)
27: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/1
27: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/1 (1 ms)
27: [----------] 2 tests from WithParameters/BiasStateTest (2 ms total)
27:
27: [----------] Global test environment tear-down
27: [==========] 12 tests from 4 test cases ran. (35 ms total)
27: [ PASSED ] 12 tests.
27/52 Test #27: AwhTest ............................. Passed 0.10 sec
test 28
Start 28: SimdUnitTests
28: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/simd-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/SimdUnitTests.xml"
28: Test timeout computed to be: 30
28: [==========] Running 86 tests from 3 test cases.
28: [----------] Global test environment set-up.
28: [----------] 41 tests from SimdScalarTest
28: [ RUN ] SimdScalarTest.load
28: [ OK ] SimdScalarTest.load (0 ms)
28: [ RUN ] SimdScalarTest.loadU
28: [ OK ] SimdScalarTest.loadU (0 ms)
28: [ RUN ] SimdScalarTest.store
28: [ OK ] SimdScalarTest.store (0 ms)
28: [ RUN ] SimdScalarTest.storeU
28: [ OK ] SimdScalarTest.storeU (0 ms)
28: [ RUN ] SimdScalarTest.setZero
28: [ OK ] SimdScalarTest.setZero (0 ms)
28: [ RUN ] SimdScalarTest.andNot
28: [ OK ] SimdScalarTest.andNot (0 ms)
28: [ RUN ] SimdScalarTest.fma
28: [ OK ] SimdScalarTest.fma (0 ms)
28: [ RUN ] SimdScalarTest.fms
28: [ OK ] SimdScalarTest.fms (0 ms)
28: [ RUN ] SimdScalarTest.fnma
28: [ OK ] SimdScalarTest.fnma (0 ms)
28: [ RUN ] SimdScalarTest.fnms
28: [ OK ] SimdScalarTest.fnms (0 ms)
28: [ RUN ] SimdScalarTest.maskAdd
28: [ OK ] SimdScalarTest.maskAdd (0 ms)
28: [ RUN ] SimdScalarTest.maskzMul
28: [ OK ] SimdScalarTest.maskzMul (0 ms)
28: [ RUN ] SimdScalarTest.maskzFma
28: [ OK ] SimdScalarTest.maskzFma (0 ms)
28: [ RUN ] SimdScalarTest.abs
28: [ OK ] SimdScalarTest.abs (0 ms)
28: [ RUN ] SimdScalarTest.max
28: [ OK ] SimdScalarTest.max (0 ms)
28: [ RUN ] SimdScalarTest.min
28: [ OK ] SimdScalarTest.min (0 ms)
28: [ RUN ] SimdScalarTest.round
28: [ OK ] SimdScalarTest.round (0 ms)
28: [ RUN ] SimdScalarTest.trunc
28: [ OK ] SimdScalarTest.trunc (0 ms)
28: [ RUN ] SimdScalarTest.reduce
28: [ OK ] SimdScalarTest.reduce (0 ms)
28: [ RUN ] SimdScalarTest.testBits
28: [ OK ] SimdScalarTest.testBits (0 ms)
28: [ RUN ] SimdScalarTest.anyTrue
28: [ OK ] SimdScalarTest.anyTrue (0 ms)
28: [ RUN ] SimdScalarTest.selectByMask
28: [ OK ] SimdScalarTest.selectByMask (0 ms)
28: [ RUN ] SimdScalarTest.selectByNotMask
28: [ OK ] SimdScalarTest.selectByNotMask (0 ms)
28: [ RUN ] SimdScalarTest.blend
28: [ OK ] SimdScalarTest.blend (0 ms)
28: [ RUN ] SimdScalarTest.cvtR2I
28: [ OK ] SimdScalarTest.cvtR2I (0 ms)
28: [ RUN ] SimdScalarTest.cvttR2I
28: [ OK ] SimdScalarTest.cvttR2I (0 ms)
28: [ RUN ] SimdScalarTest.cvtI2R
28: [ OK ] SimdScalarTest.cvtI2R (0 ms)
28: [ RUN ] SimdScalarTest.cvtF2D
28: [ OK ] SimdScalarTest.cvtF2D (0 ms)
28: [ RUN ] SimdScalarTest.cvtD2D
28: [ OK ] SimdScalarTest.cvtD2D (0 ms)
28: [ RUN ] SimdScalarTest.loadI
28: [ OK ] SimdScalarTest.loadI (0 ms)
28: [ RUN ] SimdScalarTest.loadUI
28: [ OK ] SimdScalarTest.loadUI (0 ms)
28: [ RUN ] SimdScalarTest.storeI
28: [ OK ] SimdScalarTest.storeI (0 ms)
28: [ RUN ] SimdScalarTest.storeUI
28: [ OK ] SimdScalarTest.storeUI (0 ms)
28: [ RUN ] SimdScalarTest.andNotI
28: [ OK ] SimdScalarTest.andNotI (0 ms)
28: [ RUN ] SimdScalarTest.testBitsI
28: [ OK ] SimdScalarTest.testBitsI (0 ms)
28: [ RUN ] SimdScalarTest.selectByMaskI
28: [ OK ] SimdScalarTest.selectByMaskI (0 ms)
28: [ RUN ] SimdScalarTest.selectByNotMaskI
28: [ OK ] SimdScalarTest.selectByNotMaskI (0 ms)
28: [ RUN ] SimdScalarTest.blendI
28: [ OK ] SimdScalarTest.blendI (0 ms)
28: [ RUN ] SimdScalarTest.cvtB2IB
28: [ OK ] SimdScalarTest.cvtB2IB (0 ms)
28: [ RUN ] SimdScalarTest.cvtIB2B
28: [ OK ] SimdScalarTest.cvtIB2B (0 ms)
28: [ RUN ] SimdScalarTest.expandScalarsToTriplets
28: [ OK ] SimdScalarTest.expandScalarsToTriplets (0 ms)
28: [----------] 41 tests from SimdScalarTest (1 ms total)
28:
28: [----------] 8 tests from SimdScalarUtilTest
28: [ RUN ] SimdScalarUtilTest.gatherLoadTranspose
28: [ OK ] SimdScalarUtilTest.gatherLoadTranspose (0 ms)
28: [ RUN ] SimdScalarUtilTest.gatherLoadUTranspose
28: [ OK ] SimdScalarUtilTest.gatherLoadUTranspose (0 ms)
28: [ RUN ] SimdScalarUtilTest.transposeScatterStoreU
28: [ OK ] SimdScalarUtilTest.transposeScatterStoreU (0 ms)
28: [ RUN ] SimdScalarUtilTest.transposeScatterIncrU
28: [ OK ] SimdScalarUtilTest.transposeScatterIncrU (0 ms)
28: [ RUN ] SimdScalarUtilTest.transposeScatterDecrU
28: [ OK ] SimdScalarUtilTest.transposeScatterDecrU (0 ms)
28: [ RUN ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose
28: [ OK ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose (0 ms)
28: [ RUN ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose
28: [ OK ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose (0 ms)
28: [ RUN ] SimdScalarUtilTest.reduceIncr4ReturnSum
28: [ OK ] SimdScalarUtilTest.reduceIncr4ReturnSum (0 ms)
28: [----------] 8 tests from SimdScalarUtilTest (1 ms total)
28:
28: [----------] 37 tests from SimdScalarMathTest
28: [ RUN ] SimdScalarMathTest.copysign
28: [ OK ] SimdScalarMathTest.copysign (0 ms)
28: [ RUN ] SimdScalarMathTest.invsqrtPair
28: [ OK ] SimdScalarMathTest.invsqrtPair (0 ms)
28: [ RUN ] SimdScalarMathTest.inv
28: [ OK ] SimdScalarMathTest.inv (0 ms)
28: [ RUN ] SimdScalarMathTest.maskzInvsqrt
28: [ OK ] SimdScalarMathTest.maskzInvsqrt (0 ms)
28: [ RUN ] SimdScalarMathTest.log
28: [ OK ] SimdScalarMathTest.log (0 ms)
28: [ RUN ] SimdScalarMathTest.exp2
28: [ OK ] SimdScalarMathTest.exp2 (0 ms)
28: [ RUN ] SimdScalarMathTest.exp
28: [ OK ] SimdScalarMathTest.exp (0 ms)
28: [ RUN ] SimdScalarMathTest.erf
28: [ OK ] SimdScalarMathTest.erf (0 ms)
28: [ RUN ] SimdScalarMathTest.erfc
28: [ OK ] SimdScalarMathTest.erfc (0 ms)
28: [ RUN ] SimdScalarMathTest.sincos
28: [ OK ] SimdScalarMathTest.sincos (0 ms)
28: [ RUN ] SimdScalarMathTest.sin
28: [ OK ] SimdScalarMathTest.sin (0 ms)
28: [ RUN ] SimdScalarMathTest.cos
28: [ OK ] SimdScalarMathTest.cos (0 ms)
28: [ RUN ] SimdScalarMathTest.tan
28: [ OK ] SimdScalarMathTest.tan (0 ms)
28: [ RUN ] SimdScalarMathTest.asin
28: [ OK ] SimdScalarMathTest.asin (0 ms)
28: [ RUN ] SimdScalarMathTest.acos
28: [ OK ] SimdScalarMathTest.acos (0 ms)
28: [ RUN ] SimdScalarMathTest.atan
28: [ OK ] SimdScalarMathTest.atan (0 ms)
28: [ RUN ] SimdScalarMathTest.atan2
28: [ OK ] SimdScalarMathTest.atan2 (0 ms)
28: [ RUN ] SimdScalarMathTest.pmeForceCorrection
28: [ OK ] SimdScalarMathTest.pmeForceCorrection (0 ms)
28: [ RUN ] SimdScalarMathTest.pmePotentialCorrection
28: [ OK ] SimdScalarMathTest.pmePotentialCorrection (0 ms)
28: [ RUN ] SimdScalarMathTest.invsqrtPairSingleAccuracy
28: [ OK ] SimdScalarMathTest.invsqrtPairSingleAccuracy (0 ms)
28: [ RUN ] SimdScalarMathTest.invSingleAccuracy
28: [ OK ] SimdScalarMathTest.invSingleAccuracy (0 ms)
28: [ RUN ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy
28: [ OK ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy (0 ms)
28: [ RUN ] SimdScalarMathTest.logSingleAccuracy
28: [ OK ] SimdScalarMathTest.logSingleAccuracy (0 ms)
28: [ RUN ] SimdScalarMathTest.exp2SingleAccuracy
28: [ OK ] SimdScalarMathTest.exp2SingleAccuracy (0 ms)
28: [ RUN ] SimdScalarMathTest.expSingleAccuracy
28: [ OK ] SimdScalarMathTest.expSingleAccuracy (0 ms)
28: [ RUN ] SimdScalarMathTest.erfSingleAccuracy
28: [ OK ] SimdScalarMathTest.erfSingleAccuracy (0 ms)
28: [ RUN ] SimdScalarMathTest.erfcSingleAccuracy
28: [ OK ] SimdScalarMathTest.erfcSingleAccuracy (0 ms)
28: [ RUN ] SimdScalarMathTest.sincosSingleAccuracy
28: [ OK ] SimdScalarMathTest.sincosSingleAccuracy (0 ms)
28: [ RUN ] SimdScalarMathTest.sinSingleAccuracy
28: [ OK ] SimdScalarMathTest.sinSingleAccuracy (0 ms)
28: [ RUN ] SimdScalarMathTest.cosSingleAccuracy
28: [ OK ] SimdScalarMathTest.cosSingleAccuracy (0 ms)
28: [ RUN ] SimdScalarMathTest.tanSingleAccuracy
28: [ OK ] SimdScalarMathTest.tanSingleAccuracy (0 ms)
28: [ RUN ] SimdScalarMathTest.asinSingleAccuracy
28: [ OK ] SimdScalarMathTest.asinSingleAccuracy (0 ms)
28: [ RUN ] SimdScalarMathTest.acosSingleAccuracy
28: [ OK ] SimdScalarMathTest.acosSingleAccuracy (0 ms)
28: [ RUN ] SimdScalarMathTest.atanSingleAccuracy
28: [ OK ] SimdScalarMathTest.atanSingleAccuracy (0 ms)
28: [ RUN ] SimdScalarMathTest.atan2SingleAccuracy
28: [ OK ] SimdScalarMathTest.atan2SingleAccuracy (0 ms)
28: [ RUN ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy
28: [ OK ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy (0 ms)
28: [ RUN ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy
28: [ OK ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy (0 ms)
28: [----------] 37 tests from SimdScalarMathTest (1 ms total)
28:
28: [----------] Global test environment tear-down
28: [==========] 86 tests from 3 test cases ran. (4 ms total)
28: [ PASSED ] 86 tests.
28/52 Test #28: SimdUnitTests ....................... Passed 0.07 sec
test 29
Start 29: CompatibilityHelpersTests
29: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/compat-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/CompatibilityHelpersTests.xml"
29: Test timeout computed to be: 30
29: [==========] Running 170 tests from 12 test cases.
29: [----------] Global test environment set-up.
29: [----------] 45 tests from OptionalTest
29: [ RUN ] OptionalTest.UnionCanContainNonPodTypes
29: [ OK ] OptionalTest.UnionCanContainNonPodTypes (0 ms)
29: [ RUN ] OptionalTest.CanDefaultConstructEmpty
29: [ OK ] OptionalTest.CanDefaultConstructEmpty (0 ms)
29: [ RUN ] OptionalTest.CanConstructFromNullopt
29: [ OK ] OptionalTest.CanConstructFromNullopt (0 ms)
29: [ RUN ] OptionalTest.CanDefaultConstructUsingNonDefaultConstructibleType
29: [ OK ] OptionalTest.CanDefaultConstructUsingNonDefaultConstructibleType (0 ms)
29: [ RUN ] OptionalTest.CanCopyConstructFromEmptyOptional
29: [ OK ] OptionalTest.CanCopyConstructFromEmptyOptional (1 ms)
29: [ RUN ] OptionalTest.CanMoveConstructFromEmptyOptional
29: [ OK ] OptionalTest.CanMoveConstructFromEmptyOptional (0 ms)
29: [ RUN ] OptionalTest.CanCopyConstructFromEmptyOptionalWithExplicitConversion
29: [ OK ] OptionalTest.CanCopyConstructFromEmptyOptionalWithExplicitConversion (0 ms)
29: [ RUN ] OptionalTest.CanCopyConstructFromEmptyOptionalNonExplicitConverting
29: [ OK ] OptionalTest.CanCopyConstructFromEmptyOptionalNonExplicitConverting (0 ms)
29: [ RUN ] OptionalTest.CanMoveConstructFromEmptyOptionalExplicitConverting
29: [ OK ] OptionalTest.CanMoveConstructFromEmptyOptionalExplicitConverting (0 ms)
29: [ RUN ] OptionalTest.CanMoveConstructFromEmptyOptionalNonExplicitConverting
29: [ OK ] OptionalTest.CanMoveConstructFromEmptyOptionalNonExplicitConverting (0 ms)
29: [ RUN ] OptionalTest.CanCopyConstructFromNonEmptyOptional
29: [ OK ] OptionalTest.CanCopyConstructFromNonEmptyOptional (0 ms)
29: [ RUN ] OptionalTest.CanCopyConstructFromNonEmptyOptionalExplicitConverting
29: [ OK ] OptionalTest.CanCopyConstructFromNonEmptyOptionalExplicitConverting (0 ms)
29: [ RUN ] OptionalTest.CanCopyConstructFromNonEmptyOptionalNonExplicitConverting
29: [ OK ] OptionalTest.CanCopyConstructFromNonEmptyOptionalNonExplicitConverting (0 ms)
29: [ RUN ] OptionalTest.CanMoveConstructFromNonEmptyOptional
29: [ OK ] OptionalTest.CanMoveConstructFromNonEmptyOptional (0 ms)
29: [ RUN ] OptionalTest.CanMoveConstructFromNonEmptyOptionalExplicitConverting
29: [ OK ] OptionalTest.CanMoveConstructFromNonEmptyOptionalExplicitConverting (0 ms)
29: [ RUN ] OptionalTest.CanMoveConstructFromNonEmptyOptionalNonExplicitConverting
29: [ OK ] OptionalTest.CanMoveConstructFromNonEmptyOptionalNonExplicitConverting (0 ms)
29: [ RUN ] OptionalTest.CanCopyConstructFromLiteral
29: [ OK ] OptionalTest.CanCopyConstructFromLiteral (1 ms)
29: [ RUN ] OptionalTest.CanCopyConstructFromLiteralConverting
29: [ OK ] OptionalTest.CanCopyConstructFromLiteralConverting (0 ms)
29: [ RUN ] OptionalTest.CanCopyConstructFromValue
29: [ OK ] OptionalTest.CanCopyConstructFromValue (0 ms)
29: [ RUN ] OptionalTest.CanCopyConstructFromValueConverting
29: [ OK ] OptionalTest.CanCopyConstructFromValueConverting (0 ms)
29: [ RUN ] OptionalTest.CanMoveConstructFromValue
29: [ OK ] OptionalTest.CanMoveConstructFromValue (0 ms)
29: [ RUN ] OptionalTest.CanMoveConstructFromValueExplicitConverting
29: [ OK ] OptionalTest.CanMoveConstructFromValueExplicitConverting (0 ms)
29: [ RUN ] OptionalTest.CanMoveConstructFromValueNonExplicitConverting
29: [ OK ] OptionalTest.CanMoveConstructFromValueNonExplicitConverting (0 ms)
29: [ RUN ] OptionalTest.CanInPlaceConstructFromLiteral
29: [ OK ] OptionalTest.CanInPlaceConstructFromLiteral (0 ms)
29: [ RUN ] OptionalTest.CanInPlaceCopyConstructFromValue
29: [ OK ] OptionalTest.CanInPlaceCopyConstructFromValue (0 ms)
29: [ RUN ] OptionalTest.CanInPlaceMoveConstructFromValue
29: [ OK ] OptionalTest.CanInPlaceMoveConstructFromValue (0 ms)
29: [ RUN ] OptionalTest.CanInPlaceCopyConstructFromInitializerList
29: [ OK ] OptionalTest.CanInPlaceCopyConstructFromInitializerList (0 ms)
29: [ RUN ] OptionalTest.CanInPlaceMoveConstructFromInitializerList
29: [ OK ] OptionalTest.CanInPlaceMoveConstructFromInitializerList (0 ms)
29: [ RUN ] OptionalTest.CanAssignNulloptToDisengage
29: [ OK ] OptionalTest.CanAssignNulloptToDisengage (0 ms)
29: [ RUN ] OptionalTest.CanCopyAssignBetweenEngagedAndDisengagedOptionals
29: [ OK ] OptionalTest.CanCopyAssignBetweenEngagedAndDisengagedOptionals (0 ms)
29: [ RUN ] OptionalTest.CanCopyAssignBetweenEngagedAndDisengagedOptionalsConverting
29: [ OK ] OptionalTest.CanCopyAssignBetweenEngagedAndDisengagedOptionalsConverting (1 ms)
29: [ RUN ] OptionalTest.CanMoveAssignBetweenEngagedAndDisengagedOptionalsConverting
29: [ OK ] OptionalTest.CanMoveAssignBetweenEngagedAndDisengagedOptionalsConverting (0 ms)
29: [ RUN ] OptionalTest.CanCopyAssignFromLiteral
29: [ OK ] OptionalTest.CanCopyAssignFromLiteral (0 ms)
29: [ RUN ] OptionalTest.CanCopyAssignFromValue
29: [ OK ] OptionalTest.CanCopyAssignFromValue (0 ms)
29: [ RUN ] OptionalTest.CanMoveAssignFromValue
29: [ OK ] OptionalTest.CanMoveAssignFromValue (0 ms)
29: [ RUN ] OptionalTest.CanCopyEmplaceFromArguments
29: [ OK ] OptionalTest.CanCopyEmplaceFromArguments (0 ms)
29: [ RUN ] OptionalTest.CanMoveEmplaceFromArguments
29: [ OK ] OptionalTest.CanMoveEmplaceFromArguments (0 ms)
29: [ RUN ] OptionalTest.CanCopyEmplaceFromInitializerListAndArguments
29: [ OK ] OptionalTest.CanCopyEmplaceFromInitializerListAndArguments (0 ms)
29: [ RUN ] OptionalTest.CanMoveEmplaceFromInitializerListAndArguments
29: [ OK ] OptionalTest.CanMoveEmplaceFromInitializerListAndArguments (0 ms)
29: [ RUN ] OptionalTest.CanResetContent
29: [ OK ] OptionalTest.CanResetContent (0 ms)
29: [ RUN ] OptionalTest.ProvidesRelationalOperators
29: [ OK ] OptionalTest.ProvidesRelationalOperators (1 ms)
29: [ RUN ] OptionalTest.ProvidesMixedTypeRelationalOperators
29: [ OK ] OptionalTest.ProvidesMixedTypeRelationalOperators (0 ms)
29: [ RUN ] OptionalTest.CanProduceHash
29: [ OK ] OptionalTest.CanProduceHash (0 ms)
29: [ RUN ] OptionalTest.ShowAlignmentDependingOnBaseType
29: alignment_of<char>: 1
29: alignment_of<short>: 2
29: alignment_of<int>: 4
29: alignment_of<long>: 4
29: alignment_of<float>: 4
29: alignment_of<double>: 8
29: alignment_of<long double>: 8
29: alignment_of<Struct>: 1
29: [ OK ] OptionalTest.ShowAlignmentDependingOnBaseType (0 ms)
29: [ RUN ] OptionalTest.ShowSizeDependingOnBaseType
29: sizeof( nonstd::optional_lite::detail::storage_t<char> ): 1
29: sizeof( optional<char> ): 2 (1)
29: sizeof( optional<short> ): 4 (2)
29: sizeof( optional<int> ): 8 (4)
29: sizeof( optional<long> ): 8 (4)
29: sizeof( optional<float> ): 8 (4)
29: sizeof( optional<double> ): 16 (8)
29: sizeof( optional<long double> ): 16 (8)
29: sizeof( optional<Struct> ): 2 (1)
29: [ OK ] OptionalTest.ShowSizeDependingOnBaseType (0 ms)
29: [----------] 45 tests from OptionalTest (4 ms total)
29:
29: [----------] 7 tests from MakeOptionalTest
29: [ RUN ] MakeOptionalTest.CanMoveAssignBetweenEngagedAndDisengagedOptionals
29: [ OK ] MakeOptionalTest.CanMoveAssignBetweenEngagedAndDisengagedOptionals (0 ms)
29: [ RUN ] MakeOptionalTest.CanCopyConstruct
29: [ OK ] MakeOptionalTest.CanCopyConstruct (0 ms)
29: [ RUN ] MakeOptionalTest.CanMoveConstruct
29: [ OK ] MakeOptionalTest.CanMoveConstruct (0 ms)
29: [ RUN ] MakeOptionalTest.CanInPlaceCopyConstructFromArguments
29: [ OK ] MakeOptionalTest.CanInPlaceCopyConstructFromArguments (0 ms)
29: [ RUN ] MakeOptionalTest.CanInPlaceMoveConstructFromArguments
29: [ OK ] MakeOptionalTest.CanInPlaceMoveConstructFromArguments (0 ms)
29: [ RUN ] MakeOptionalTest.CanInPlaceCopyConstructFromInitializerListAndArguments
29: [ OK ] MakeOptionalTest.CanInPlaceCopyConstructFromInitializerListAndArguments (0 ms)
29: [ RUN ] MakeOptionalTest.CanInPlaceMoveConstructFromInitializerListAndArguments
29: [ OK ] MakeOptionalTest.CanInPlaceMoveConstructFromInitializerListAndArguments (0 ms)
29: [----------] 7 tests from MakeOptionalTest (0 ms total)
29:
29: [----------] 4 tests from OptionalMemberSwapTest
29: [ RUN ] OptionalMemberSwapTest.CanSwapDisengagedWithDisengaged
29: [ OK ] OptionalMemberSwapTest.CanSwapDisengagedWithDisengaged (0 ms)
29: [ RUN ] OptionalMemberSwapTest.CanSwapEngagedWithDisengaged
29: [ OK ] OptionalMemberSwapTest.CanSwapEngagedWithDisengaged (0 ms)
29: [ RUN ] OptionalMemberSwapTest.CanSwapDisengagedWithEngaged
29: [ OK ] OptionalMemberSwapTest.CanSwapDisengagedWithEngaged (0 ms)
29: [ RUN ] OptionalMemberSwapTest.CanSwapEngagedWithEngaged
29: [ OK ] OptionalMemberSwapTest.CanSwapEngagedWithEngaged (0 ms)
29: [----------] 4 tests from OptionalMemberSwapTest (0 ms total)
29:
29: [----------] 4 tests from OptionalImplicitValueTest
29: [ RUN ] OptionalImplicitValueTest.CanObtainValueConst
29: [ OK ] OptionalImplicitValueTest.CanObtainValueConst (0 ms)
29: [ RUN ] OptionalImplicitValueTest.CanObtainValueNonConst
29: [ OK ] OptionalImplicitValueTest.CanObtainValueNonConst (0 ms)
29: [ RUN ] OptionalImplicitValueTest.CanObtainMovedFromValueConst
29: [ OK ] OptionalImplicitValueTest.CanObtainMovedFromValueConst (0 ms)
29: [ RUN ] OptionalImplicitValueTest.CanObtainMovedFromValueNonConst
29: [ OK ] OptionalImplicitValueTest.CanObtainMovedFromValueNonConst (0 ms)
29: [----------] 4 tests from OptionalImplicitValueTest (0 ms total)
29:
29: [----------] 20 tests from OptionalIntValueTest
29: [ RUN ] OptionalIntValueTest.CanObtainValueFromDereferenceOperatorConst
29: [ OK ] OptionalIntValueTest.CanObtainValueFromDereferenceOperatorConst (0 ms)
29: [ RUN ] OptionalIntValueTest.CanObtainValueFromDereferenceOperatorNonConst
29: [ OK ] OptionalIntValueTest.CanObtainValueFromDereferenceOperatorNonConst (0 ms)
29: [ RUN ] OptionalIntValueTest.CanObtainMovedValueFromDereferenceOperatorConst
29: [ OK ] OptionalIntValueTest.CanObtainMovedValueFromDereferenceOperatorConst (0 ms)
29: [ RUN ] OptionalIntValueTest.CanObtainMovedValueFromDereferenceOperatorNonConst
29: [ OK ] OptionalIntValueTest.CanObtainMovedValueFromDereferenceOperatorNonConst (0 ms)
29: [ RUN ] OptionalIntValueTest.CanObtainHasValueViaOperatorBool
29: [ OK ] OptionalIntValueTest.CanObtainHasValueViaOperatorBool (0 ms)
29: [ RUN ] OptionalIntValueTest.CanObtainValueViaValueMethodConst
29: [ OK ] OptionalIntValueTest.CanObtainValueViaValueMethodConst (0 ms)
29: [ RUN ] OptionalIntValueTest.CanObtainValueViaValueMethodNonConst
29: [ OK ] OptionalIntValueTest.CanObtainValueViaValueMethodNonConst (0 ms)
29: [ RUN ] OptionalIntValueTest.CanObtainMovedValueViaValueMethodConst
29: [ OK ] OptionalIntValueTest.CanObtainMovedValueViaValueMethodConst (0 ms)
29: [ RUN ] OptionalIntValueTest.CanObtainMovedValueViaValueMethodNonConst
29: [ OK ] OptionalIntValueTest.CanObtainMovedValueViaValueMethodNonConst (0 ms)
29: [ RUN ] OptionalIntValueTest.CanObtainValueFromNonEmptyOptionalViaValueOrMethod
29: [ OK ] OptionalIntValueTest.CanObtainValueFromNonEmptyOptionalViaValueOrMethod (0 ms)
29: [ RUN ] OptionalIntValueTest.CanObtainDefaultFromEmptyOptionalViaValueOrMethod
29: [ OK ] OptionalIntValueTest.CanObtainDefaultFromEmptyOptionalViaValueOrMethod (0 ms)
29: [ RUN ] OptionalIntValueTest.CanObtainMovedFromValueForLValuesViaValueOrMethod
29: [ OK ] OptionalIntValueTest.CanObtainMovedFromValueForLValuesViaValueOrMethod (0 ms)
29: [ RUN ] OptionalIntValueTest.CanObtainMovedFromValueForRValuesViaValueOrMethod
29: [ OK ] OptionalIntValueTest.CanObtainMovedFromValueForRValuesViaValueOrMethod (0 ms)
29: [ RUN ] OptionalIntValueTest.ThrowsBadOptionalAccessAtDisengagedAccessForLValues
29: [ OK ] OptionalIntValueTest.ThrowsBadOptionalAccessAtDisengagedAccessForLValues (0 ms)
29: [ RUN ] OptionalIntValueTest.ThrowsBadOptionalAccessAtDisengagedAccessForRValues
29: [ OK ] OptionalIntValueTest.ThrowsBadOptionalAccessAtDisengagedAccessForRValues (0 ms)
29: [ RUN ] OptionalIntValueTest.ThrowsBadOptionalAccessWithNonEmptyWhatMethod
29: [ OK ] OptionalIntValueTest.ThrowsBadOptionalAccessWithNonEmptyWhatMethod (0 ms)
29: [ RUN ] OptionalIntValueTest.CanNonMemberSwapDisengagnedWithDisengaged
29: [ OK ] OptionalIntValueTest.CanNonMemberSwapDisengagnedWithDisengaged (0 ms)
29: [ RUN ] OptionalIntValueTest.CanNonMemberSwapEngagnedWithEngaged
29: [ OK ] OptionalIntValueTest.CanNonMemberSwapEngagnedWithEngaged (0 ms)
29: [ RUN ] OptionalIntValueTest.CanNonMemberSwapDisengagnedWithEngaged
29: [ OK ] OptionalIntValueTest.CanNonMemberSwapDisengagnedWithEngaged (0 ms)
29: [ RUN ] OptionalIntValueTest.CanNonMemberSwapEngagnedWithDisengaged
29: [ OK ] OptionalIntValueTest.CanNonMemberSwapEngagnedWithDisengaged (0 ms)
29: [----------] 20 tests from OptionalIntValueTest (2 ms total)
29:
29: [----------] 1 test from NotNullConstruction
29: [ RUN ] NotNullConstruction.Works
29: [ OK ] NotNullConstruction.Works (0 ms)
29: [----------] 1 test from NotNullConstruction (0 ms total)
29:
29: [----------] 1 test from NotNullCasting
29: [ RUN ] NotNullCasting.Works
29: [ OK ] NotNullCasting.Works (0 ms)
29: [----------] 1 test from NotNullCasting (0 ms total)
29:
29: [----------] 1 test from NotNullAssignment
29: [ RUN ] NotNullAssignment.Works
29: [ OK ] NotNullAssignment.Works (0 ms)
29: [----------] 1 test from NotNullAssignment (0 ms total)
29:
29: [----------] 1 test from MakeNotNull
29: [ RUN ] MakeNotNull.Works
29: [ OK ] MakeNotNull.Works (0 ms)
29: [----------] 1 test from MakeNotNull (0 ms total)
29:
29: [----------] 1 test from NotNull
29: [ RUN ] NotNull.WorksInContainers
29: [ OK ] NotNull.WorksInContainers (0 ms)
29: [----------] 1 test from NotNull (0 ms total)
29:
29: [----------] 80 tests from StringViewTest
29: [ RUN ] StringViewTest.CanDefaultConstructEmptyView
29: [ OK ] StringViewTest.CanDefaultConstructEmptyView (0 ms)
29: [ RUN ] StringViewTest.CanConstructFromPointerAndSize
29: [ OK ] StringViewTest.CanConstructFromPointerAndSize (0 ms)
29: [ RUN ] StringViewTest.CanConstructFromCString
29: [ OK ] StringViewTest.CanConstructFromCString (0 ms)
29: [ RUN ] StringViewTest.CanCopyConstructFromEmptyView
29: [ OK ] StringViewTest.CanCopyConstructFromEmptyView (0 ms)
29: [ RUN ] StringViewTest.CanCopyConstructFromNonEmptyView
29: [ OK ] StringViewTest.CanCopyConstructFromNonEmptyView (0 ms)
29: [ RUN ] StringViewTest.CanCopyAssingFromEmptyView
29: [ OK ] StringViewTest.CanCopyAssingFromEmptyView (0 ms)
29: [ RUN ] StringViewTest.CanCopyAssingFromNonEmptyView
29: [ OK ] StringViewTest.CanCopyAssingFromNonEmptyView (0 ms)
29: [ RUN ] StringViewTest.AllowForwardIteration
29: [ OK ] StringViewTest.AllowForwardIteration (0 ms)
29: [ RUN ] StringViewTest.AllowConstForwardIteration
29: [ OK ] StringViewTest.AllowConstForwardIteration (0 ms)
29: [ RUN ] StringViewTest.AllowReverseIteration
29: [ OK ] StringViewTest.AllowReverseIteration (0 ms)
29: [ RUN ] StringViewTest.AllowConstReverseIteration
29: [ OK ] StringViewTest.AllowConstReverseIteration (0 ms)
29: [ RUN ] StringViewTest.CanObtainSizeFromViewViaSize
29: [ OK ] StringViewTest.CanObtainSizeFromViewViaSize (0 ms)
29: [ RUN ] StringViewTest.CanObtainSizeFromViewViaLength
29: [ OK ] StringViewTest.CanObtainSizeFromViewViaLength (0 ms)
29: [ RUN ] StringViewTest.CanObtainMaxSizeViaMaxSize
29: [ OK ] StringViewTest.CanObtainMaxSizeViaMaxSize (0 ms)
29: [ RUN ] StringViewTest.CanCheckForEmptyStringWithEmpty
29: [ OK ] StringViewTest.CanCheckForEmptyStringWithEmpty (0 ms)
29: [ RUN ] StringViewTest.CanAccessElementViaArrayIndex
29: [ OK ] StringViewTest.CanAccessElementViaArrayIndex (0 ms)
29: [ RUN ] StringViewTest.CanAccessElementViaAt
29: [ OK ] StringViewTest.CanAccessElementViaAt (0 ms)
29: [ RUN ] StringViewTest.ThrowsOnOutOfBoundsAccess
29: [ OK ] StringViewTest.ThrowsOnOutOfBoundsAccess (0 ms)
29: [ RUN ] StringViewTest.CanAccessAllElementsViaData
29: [ OK ] StringViewTest.CanAccessAllElementsViaData (1 ms)
29: [ RUN ] StringViewTest.DataFromEmptyStringIsNullptr
29: [ OK ] StringViewTest.DataFromEmptyStringIsNullptr (0 ms)
29: [ RUN ] StringViewTest.CanRemovePrefix
29: [ OK ] StringViewTest.CanRemovePrefix (0 ms)
29: [ RUN ] StringViewTest.CanRemoveSuffix
29: [ OK ] StringViewTest.CanRemoveSuffix (0 ms)
29: [ RUN ] StringViewTest.CanSwapWithOtherView
29: [ OK ] StringViewTest.CanSwapWithOtherView (0 ms)
29: [ RUN ] StringViewTest.CanCopySubstringWithCopy
29: [ OK ] StringViewTest.CanCopySubstringWithCopy (0 ms)
29: [ RUN ] StringViewTest.ThrowsOnOutOfBoundsCopy
29: [ OK ] StringViewTest.ThrowsOnOutOfBoundsCopy (0 ms)
29: [ RUN ] StringViewTest.CanObtainSubstringWithSubstr
29: [ OK ] StringViewTest.CanObtainSubstringWithSubstr (0 ms)
29: [ RUN ] StringViewTest.ThrowsOnOutOfBoundsSubstr
29: [ OK ] StringViewTest.ThrowsOnOutOfBoundsSubstr (0 ms)
29: [ RUN ] StringViewTest.CanLexicallyCompareViewWithCompare
29: [ OK ] StringViewTest.CanLexicallyCompareViewWithCompare (0 ms)
29: [ RUN ] StringViewTest.CanCompareEmptyViewsWIthCompare
29: [ OK ] StringViewTest.CanCompareEmptyViewsWIthCompare (0 ms)
29: [ RUN ] StringViewTest.CanCompareSubStringWithViewViaCompare
29: [ OK ] StringViewTest.CanCompareSubStringWithViewViaCompare (0 ms)
29: [ RUN ] StringViewTest.CanCompareSubStringWithSubStringViewViaCompare
29: [ OK ] StringViewTest.CanCompareSubStringWithSubStringViewViaCompare (0 ms)
29: [ RUN ] StringViewTest.CanCompareToCStringViaCompare
29: [ OK ] StringViewTest.CanCompareToCStringViaCompare (0 ms)
29: [ RUN ] StringViewTest.CanCompareSubStringToCStringViaCompare
29: [ OK ] StringViewTest.CanCompareSubStringToCStringViaCompare (0 ms)
29: [ RUN ] StringViewTest.CanCompareSubStringToCStringPrefixViaCompare
29: [ OK ] StringViewTest.CanCompareSubStringToCStringPrefixViaCompare (0 ms)
29: [ RUN ] StringViewTest.CanCheckForPrefixViewViaStartsWith
29: [ OK ] StringViewTest.CanCheckForPrefixViewViaStartsWith (0 ms)
29: [ RUN ] StringViewTest.CanCheckForPrefixCharacterViaStartsWith
29: [ OK ] StringViewTest.CanCheckForPrefixCharacterViaStartsWith (0 ms)
29: [ RUN ] StringViewTest.CanCheckForPrefixCStringViaStartsWith
29: [ OK ] StringViewTest.CanCheckForPrefixCStringViaStartsWith (0 ms)
29: [ RUN ] StringViewTest.CanCheckForSuffixViewViaEndsWith
29: [ OK ] StringViewTest.CanCheckForSuffixViewViaEndsWith (0 ms)
29: [ RUN ] StringViewTest.CanCheckForSuffixCharacterViaEndsWith
29: [ OK ] StringViewTest.CanCheckForSuffixCharacterViaEndsWith (0 ms)
29: [ RUN ] StringViewTest.CanCheckForSuffixCStringViaEndsWith
29: [ OK ] StringViewTest.CanCheckForSuffixCStringViaEndsWith (0 ms)
29: [ RUN ] StringViewTest.CanSearchForViewSubstrViaFind
29: [ OK ] StringViewTest.CanSearchForViewSubstrViaFind (0 ms)
29: [ RUN ] StringViewTest.CanSearchForCharacterViaFind
29: [ OK ] StringViewTest.CanSearchForCharacterViaFind (0 ms)
29: [ RUN ] StringViewTest.CanSearchForCStringSubstringViaFind
29: [ OK ] StringViewTest.CanSearchForCStringSubstringViaFind (0 ms)
29: [ RUN ] StringViewTest.CanSearchForCStringSubstringViaFindWithDefaultPos
29: [ OK ] StringViewTest.CanSearchForCStringSubstringViaFindWithDefaultPos (0 ms)
29: [ RUN ] StringViewTest.CanBackwardsSearchForViewSubstrViaFind
29: [ OK ] StringViewTest.CanBackwardsSearchForViewSubstrViaFind (0 ms)
29: [ RUN ] StringViewTest.CanBackwardsSearchForCharacterViaFind
29: [ OK ] StringViewTest.CanBackwardsSearchForCharacterViaFind (0 ms)
29: [ RUN ] StringViewTest.CanBackwardsSearchForCStringSubstringViaFind
29: [ OK ] StringViewTest.CanBackwardsSearchForCStringSubstringViaFind (0 ms)
29: [ RUN ] StringViewTest.CanBackwardsSearchForCStringSubstringViaFindWithDefaultPos
29: [ OK ] StringViewTest.CanBackwardsSearchForCStringSubstringViaFindWithDefaultPos (1 ms)
29: [ RUN ] StringViewTest.CanSearchForFirstOccurenceOfAnyCharacterInView
29: [ OK ] StringViewTest.CanSearchForFirstOccurenceOfAnyCharacterInView (0 ms)
29: [ RUN ] StringViewTest.CanSearchForFirstOccurenceOfCharacter
29: [ OK ] StringViewTest.CanSearchForFirstOccurenceOfCharacter (0 ms)
29: [ RUN ] StringViewTest.CanSearchForFirstOccurenceOfCharactersInCStringInLenght
29: [ OK ] StringViewTest.CanSearchForFirstOccurenceOfCharactersInCStringInLenght (0 ms)
29: [ RUN ] StringViewTest.CanSearchForFirstOccurenceOfCharactersInCString
29: [ OK ] StringViewTest.CanSearchForFirstOccurenceOfCharactersInCString (0 ms)
29: [ RUN ] StringViewTest.CanBackwardsSearchForLastOccurenceOfAnyCharacterInView
29: [ OK ] StringViewTest.CanBackwardsSearchForLastOccurenceOfAnyCharacterInView (0 ms)
29: [ RUN ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharacter
29: [ OK ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharacter (0 ms)
29: [ RUN ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharactersInCStringInLenght
29: [ OK ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharactersInCStringInLenght (0 ms)
29: [ RUN ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharactersInCString
29: [ OK ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharactersInCString (0 ms)
29: [ RUN ] StringViewTest.CanSearchForFirstNotFoundCharacter
29: [ OK ] StringViewTest.CanSearchForFirstNotFoundCharacter (0 ms)
29: [ RUN ] StringViewTest.CanSearchForFirstNonMatchingCharacter
29: [ OK ] StringViewTest.CanSearchForFirstNonMatchingCharacter (0 ms)
29: [ RUN ] StringViewTest.CanSearchForFirstNonEqualToAnyCharacterInCStringInLength
29: [ OK ] StringViewTest.CanSearchForFirstNonEqualToAnyCharacterInCStringInLength (0 ms)
29: [ RUN ] StringViewTest.CanSearchForFirstNonEqualToAnyCharacterInCString
29: [ OK ] StringViewTest.CanSearchForFirstNonEqualToAnyCharacterInCString (0 ms)
29: [ RUN ] StringViewTest.CanBackwardsSearchForForstNonFoundCharacterInView
29: [ OK ] StringViewTest.CanBackwardsSearchForForstNonFoundCharacterInView (0 ms)
29: [ RUN ] StringViewTest.CanBackwardsSearchForFirstNonMatchingCharacter
29: [ OK ] StringViewTest.CanBackwardsSearchForFirstNonMatchingCharacter (1 ms)
29: [ RUN ] StringViewTest.CanBackwardsSearchForFirstNonEqualToAnyCharacterInCStringInLength
29: [ OK ] StringViewTest.CanBackwardsSearchForFirstNonEqualToAnyCharacterInCStringInLength (0 ms)
29: [ RUN ] StringViewTest.CanBackwardsSearchForFirstNonEqualToAnyCharacterInCString
29: [ OK ] StringViewTest.CanBackwardsSearchForFirstNonEqualToAnyCharacterInCString (0 ms)
29: [ RUN ] StringViewTest.CanCreateViewWithLiteralSV
29: [ OK ] StringViewTest.CanCreateViewWithLiteralSV (0 ms)
29: [ RUN ] StringViewTest.CanCreateViewWithLiteralSVInLiteralsStringViewLiteralsNamespace
29: [ OK ] StringViewTest.CanCreateViewWithLiteralSVInLiteralsStringViewLiteralsNamespace (0 ms)
29: [ RUN ] StringViewTest.CanCreateViewWithLiteralSVInStringViewLiteralsNamespace
29: [ OK ] StringViewTest.CanCreateViewWithLiteralSVInStringViewLiteralsNamespace (0 ms)
29: [ RUN ] StringViewTest.CanCreateViewWithLiteralSVInLiteralsNamespace
29: [ OK ] StringViewTest.CanCreateViewWithLiteralSVInLiteralsNamespace (0 ms)
29: [ RUN ] StringViewTest.CanCreateViewWithLiteral_SV
29: [ OK ] StringViewTest.CanCreateViewWithLiteral_SV (0 ms)
29: [ RUN ] StringViewTest.CanCreateViewWithLiteral_SVInLiteralsStringViewLiteralsNamespace
29: [ OK ] StringViewTest.CanCreateViewWithLiteral_SVInLiteralsStringViewLiteralsNamespace (0 ms)
29: [ RUN ] StringViewTest.CanCreateViewWithLiteral_SVInStringViewLiteralsNamespace
29: [ OK ] StringViewTest.CanCreateViewWithLiteral_SVInStringViewLiteralsNamespace (0 ms)
29: [ RUN ] StringViewTest.CanCreateViewWithLiteral_SVInLiteralsNamespace
29: [ OK ] StringViewTest.CanCreateViewWithLiteral_SVInLiteralsNamespace (0 ms)
29: [ RUN ] StringViewTest.CanCompareToViews
29: [ OK ] StringViewTest.CanCompareToViews (0 ms)
29: [ RUN ] StringViewTest.CanCompareViewToImplicitlyConvertedView
29: [ OK ] StringViewTest.CanCompareViewToImplicitlyConvertedView (0 ms)
29: [ RUN ] StringViewTest.EmptyViewsCompareAsEqual
29: [ OK ] StringViewTest.EmptyViewsCompareAsEqual (0 ms)
29: [ RUN ] StringViewTest.CanPrintViewToPutputStream
29: [ OK ] StringViewTest.CanPrintViewToPutputStream (0 ms)
29: [ RUN ] StringViewTest.HashOfViewIsEqualToHashOfString
29: [ OK ] StringViewTest.HashOfViewIsEqualToHashOfString (1 ms)
29: [ RUN ] StringViewTest.HashOfWStringViewIsEqualToHashOfString
29: [ OK ] StringViewTest.HashOfWStringViewIsEqualToHashOfString (0 ms)
29: [ RUN ] StringViewTest.HashOfU16StringViewIsEqualToHashOfString
29: [ OK ] StringViewTest.HashOfU16StringViewIsEqualToHashOfString (0 ms)
29: [ RUN ] StringViewTest.HashOfU32StringViewIsEqualToHashOfString
29: [ OK ] StringViewTest.HashOfU32StringViewIsEqualToHashOfString (0 ms)
29: [----------] 80 tests from StringViewTest (6 ms total)
29:
29: [----------] 5 tests from StringViewExtensionTest
29: [ RUN ] StringViewExtensionTest.CanConstructViewFromString
29: [ OK ] StringViewExtensionTest.CanConstructViewFromString (0 ms)
29: [ RUN ] StringViewExtensionTest.CanConvertViewToStringViaExplicitOperator
29: [ OK ] StringViewExtensionTest.CanConvertViewToStringViaExplicitOperator (0 ms)
29: [ RUN ] StringViewExtensionTest.CanConvertViewToStringViaToString
29: [ OK ] StringViewExtensionTest.CanConvertViewToStringViaToString (0 ms)
29: [ RUN ] StringViewExtensionTest.CanConvertViewToStringViaToStringFreeFunction
29: [ OK ] StringViewExtensionTest.CanConvertViewToStringViaToStringFreeFunction (0 ms)
29: [ RUN ] StringViewExtensionTest.CanConvertViewToStringViewViaToStringView
29: [ OK ] StringViewExtensionTest.CanConvertViewToStringViewViaToStringView (0 ms)
29: [----------] 5 tests from StringViewExtensionTest (0 ms total)
29:
29: [----------] Global test environment tear-down
29: [==========] 170 tests from 12 test cases ran. (14 ms total)
29: [ PASSED ] 170 tests.
29/52 Test #29: CompatibilityHelpersTests ........... Passed 0.09 sec
test 30
Start 30: GmxAnaTest
30: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/gmxana-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/GmxAnaTest.xml"
30: Test timeout computed to be: 600
30: [==========] Running 27 tests from 5 test cases.
30: [----------] Global test environment set-up.
30: [----------] 5 tests from Entropy
30: [ RUN ] Entropy.Schlitter_300_NoLinear
30: [ OK ] Entropy.Schlitter_300_NoLinear (1 ms)
30: [ RUN ] Entropy.Schlitter_300_Linear
30: [ OK ] Entropy.Schlitter_300_Linear (1 ms)
30: [ RUN ] Entropy.QuasiHarmonic_300_NoLinear
30: [ OK ] Entropy.QuasiHarmonic_300_NoLinear (0 ms)
30: [ RUN ] Entropy.QuasiHarmonic_200_NoLinear
30: [ OK ] Entropy.QuasiHarmonic_200_NoLinear (0 ms)
30: [ RUN ] Entropy.QuasiHarmonic_200_Linear
30: [ OK ] Entropy.QuasiHarmonic_200_Linear (1 ms)
30: [----------] 5 tests from Entropy (3 ms total)
30:
30: [----------] 10 tests from MindistTest
30: [ RUN ] MindistTest.mindistWorksWithSingleAtoms
30: Group 0 ( atom1) has 1 elements
30: Group 1 ( atom2) has 1 elements
30: Group 2 ( atom3) has 1 elements
30: Group 3 ( atoms12) has 2 elements
30: Group 4 ( atoms23) has 2 elements
30: Group 5 ( atoms123) has 3 elements
30: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
30:
Reading frame 0 time 0.000
Last frame 0 time 0.000
30: Selected 0: 'atom1'
30: Selected 1: 'atom2'
30: [ OK ] MindistTest.mindistWorksWithSingleAtoms (7 ms)
30: [ RUN ] MindistTest.mindistWorksWithMultipleAtoms
30: Group 0 ( atom1) has 1 elements
30: Group 1 ( atom2) has 1 elements
30: Group 2 ( atom3) has 1 elements
30: Group 3 ( atoms12) has 2 elements
30: Group 4 ( atoms23) has 2 elements
30: Group 5 ( atoms123) has 3 elements
30: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
30:
Reading frame 0 time 0.000
Last frame 0 time 0.000
30: Selected 2: 'atom3'
30: Selected 3: 'atoms12'
30: [ OK ] MindistTest.mindistWorksWithMultipleAtoms (4 ms)
30: [ RUN ] MindistTest.mindistDoesNotPickUpContacts
30: Group 0 ( atom1) has 1 elements
30: Group 1 ( atom2) has 1 elements
30: Group 2 ( atom3) has 1 elements
30: Group 3 ( atoms12) has 2 elements
30: Group 4 ( atoms23) has 2 elements
30: Group 5 ( atoms123) has 3 elements
30: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
30:
Reading frame 0 time 0.000
Last frame 0 time 0.000
30: Selected 0: 'atom1'
30: Selected 1: 'atom2'
30: [ OK ] MindistTest.mindistDoesNotPickUpContacts (5 ms)
30: [ RUN ] MindistTest.mindistPicksUpContacts
30: Group 0 ( atom1) has 1 elements
30: Group 1 ( atom2) has 1 elements
30: Group 2 ( atom3) has 1 elements
30: Group 3 ( atoms12) has 2 elements
30: Group 4 ( atoms23) has 2 elements
30: Group 5 ( atoms123) has 3 elements
30: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
30:
Reading frame 0 time 0.000
Last frame 0 time 0.000
30: Selected 0: 'atom1'
30: Selected 1: 'atom2'
30: [ OK ] MindistTest.mindistPicksUpContacts (5 ms)
30: [ RUN ] MindistTest.ngWorks
30: Group 0 ( atom1) has 1 elements
30: Group 1 ( atom2) has 1 elements
30: Group 2 ( atom3) has 1 elements
30: Group 3 ( atoms12) has 2 elements
30: Group 4 ( atoms23) has 2 elements
30: Group 5 ( atoms123) has 3 elements
30: Select a group: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
30:
Reading frame 0 time 0.000
Last frame 0 time 0.000
30: Selected 0: 'atom1'
30: Selected 1: 'atom2'
30: Selected 2: 'atom3'
30: [ OK ] MindistTest.ngWorks (4 ms)
30: [ RUN ] MindistTest.groupWorks
30: Group 0 ( atom1) has 1 elements
30: Group 1 ( atom2) has 1 elements
30: Group 2 ( atom3) has 1 elements
30: Group 3 ( atoms12) has 2 elements
30: Group 4 ( atoms23) has 2 elements
30: Group 5 ( atoms123) has 3 elements
30: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
30:
Reading frame 0 time 0.000
Last frame 0 time 0.000
30: Selected 3: 'atoms12'
30: Selected 2: 'atom3'
30: [ OK ] MindistTest.groupWorks (6 ms)
30: [ RUN ] MindistTest.maxDistWorks
30: Group 0 ( atom1) has 1 elements
30: Group 1 ( atom2) has 1 elements
30: Group 2 ( atom3) has 1 elements
30: Group 3 ( atoms12) has 2 elements
30: Group 4 ( atoms23) has 2 elements
30: Group 5 ( atoms123) has 3 elements
30: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
30:
Reading frame 0 time 0.000
Last frame 0 time 0.000
30: Selected 2: 'atom3'
30: Selected 3: 'atoms12'
30: [ OK ] MindistTest.maxDistWorks (4 ms)
30: [ RUN ] MindistTest.noPbcWorks
30: Group 0 ( atom1) has 1 elements
30: Group 1 ( atom2) has 1 elements
30: Group 2 ( atom3) has 1 elements
30: Group 3 ( atoms12) has 2 elements
30: Group 4 ( atoms23) has 2 elements
30: Group 5 ( atoms123) has 3 elements
30: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
30:
Reading frame 0 time 0.000
Last frame 0 time 0.000
30: Selected 0: 'atom1'
30: Selected 1: 'atom2'
30: [ OK ] MindistTest.noPbcWorks (4 ms)
30: [ RUN ] MindistTest.resPerTimeWorks
30: Group 0 ( atom1) has 1 elements
30: Group 1 ( atom2) has 1 elements
30: Group 2 ( atom3) has 1 elements
30: Group 3 ( atoms12) has 2 elements
30: Group 4 ( atoms23) has 2 elements
30: Group 5 ( atoms123) has 3 elements
30: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
30:
Reading frame 0 time 0.000
Last frame 0 time 0.000
30: Selected 3: 'atoms12'
30: Selected 2: 'atom3'
30: [ OK ] MindistTest.resPerTimeWorks (5 ms)
30: [ RUN ] MindistTest.matrixWorks
30: Group 0 ( atom1) has 1 elements
30: Group 1 ( atom2) has 1 elements
30: Group 2 ( atom3) has 1 elements
30: Group 3 ( atoms12) has 2 elements
30: Group 4 ( atoms23) has 2 elements
30: Group 5 ( atoms123) has 3 elements
30: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
30:
Reading frame 0 time 0.000
Last frame 0 time 0.000
30: Selected 5: 'atoms123'
30: Special case: making distance matrix between all atoms in group atoms123
30: [ OK ] MindistTest.matrixWorks (4 ms)
30: [----------] 10 tests from MindistTest (52 ms total)
30:
30: [----------] 3 tests from MsdTest
30: [ RUN ] MsdTest.threeDimensionalDiffusion
30:
30: Select a group to calculate mean squared displacement for:
30: Group 0 ( particles) has 3 elements
30: There is one group in the index
30:
Reading frame 0 time 0.000
Reading frame 1 time 1.000
Reading frame 2 time 2.000
Reading frame 3 time 3.000
Reading frame 4 time 4.000
Reading frame 5 time 5.000
Reading frame 6 time 6.000
Reading frame 7 time 7.000
Reading frame 8 time 8.000
Reading frame 9 time 9.000
Last frame 9 time 9.000
30:
30: Used 1 restart points spaced 200 ps over 9 ps
30:
30: Fitting from 1 to 8 ps
30:
30: D[ particles] 4.0000 (+/- 0.0000) 1e-5 cm^2/s
30: [ OK ] MsdTest.threeDimensionalDiffusion (6 ms)
30: [ RUN ] MsdTest.twoDimensionalDiffusion
30:
30: Select a group to calculate mean squared displacement for:
30: Group 0 ( particles) has 3 elements
30: There is one group in the index
30:
Reading frame 0 time 0.000
Reading frame 1 time 1.000
Reading frame 2 time 2.000
Reading frame 3 time 3.000
Reading frame 4 time 4.000
Reading frame 5 time 5.000
Reading frame 6 time 6.000
Reading frame 7 time 7.000
Reading frame 8 time 8.000
Reading frame 9 time 9.000
Last frame 9 time 9.000
30:
30: Used 1 restart points spaced 200 ps over 9 ps
30:
30: Fitting from 1 to 8 ps
30:
30: D[ particles] 6.0000 (+/- 0.0000) 1e-5 cm^2/s
30: [ OK ] MsdTest.twoDimensionalDiffusion (4 ms)
30: [ RUN ] MsdTest.oneDimensionalDiffusion
30:
30: Select a group to calculate mean squared displacement for:
30: Group 0 ( particles) has 3 elements
30: There is one group in the index
30:
Reading frame 0 time 0.000
Reading frame 1 time 1.000
Reading frame 2 time 2.000
Reading frame 3 time 3.000
Reading frame 4 time 4.000
Reading frame 5 time 5.000
Reading frame 6 time 6.000
Reading frame 7 time 7.000
Reading frame 8 time 8.000
Reading frame 9 time 9.000
Last frame 9 time 9.000
30:
30: Used 1 restart points spaced 200 ps over 9 ps
30:
30: Fitting from 1 to 8 ps
30:
30: D[ particles] 8.0000 (+/- 0.0000) 1e-5 cm^2/s
30: [ OK ] MsdTest.oneDimensionalDiffusion (5 ms)
30: [----------] 3 tests from MsdTest (15 ms total)
30:
30: [----------] 3 tests from MsdMolTest
30: [ RUN ] MsdMolTest.diffMolMassWeighted
30:
30: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.mdp]:
30: For a correct single-point energy evaluation with nsteps = 0, use
30: continuation = yes to avoid constraining the input coordinates.
30:
30: Setting the LD random seed to 405113586
30: Generated 330891 of the 330891 non-bonded parameter combinations
30: Generating 1-4 interactions: fudge = 0.5
30: Generated 330891 of the 330891 1-4 parameter combinations
30: Excluding 2 bonded neighbours molecule type 'SOL'
30: Number of degrees of freedom in T-Coupling group rest is 27.00
30:
30: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.mdp]:
30: NVE simulation with an initial temperature of zero: will use a Verlet
30: buffer of 10%. Check your energy drift!
30:
30:
30: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.mdp]:
30: You are using a plain Coulomb cut-off, which might produce artifacts.
30: You might want to consider using PME electrostatics.
30:
30:
30:
30: There were 3 notes
30: Calculating diffusion coefficients for molecules.
30: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
30: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
30:
30: Select a group to calculate mean squared displacement for:
30: Group 0 ( water) has 15 elements
30: There is one group in the index
30: Split group of 15 atoms into 5 molecules
30: Reading frames from pdb file
Reading frame 0 time 0.000 'water t= 0.00400 step= 20', 15 atoms
30:
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Reading frame 5 time 0.020
Reading frame 6 time 0.024
Reading frame 7 time 0.028
Reading frame 8 time 0.032
Reading frame 9 time 0.036
Reading frame 10 time 0.040
Reading frame 11 time 0.044
Reading frame 12 time 0.048
Reading frame 13 time 0.052
Reading frame 14 time 0.056
Reading frame 15 time 0.060
Reading frame 16 time 0.064
Reading frame 17 time 0.068
Reading frame 18 time 0.072
Reading frame 19 time 0.076
Reading frame 20 time 0.080
30:
30: Used 1 restart points spaced 200 ps over 0.1 ps
30:
30: This run will generate roughly 0 Mb of data
30: <D> = 6.4731 Std. Dev. = 8.0969 Error = 3.6210
30: Fitting from 0.008 to 0.088 ps
30:
30: D[ water] 6.5741 (+/- 0.7753) 1e-5 cm^2/s
30: [ OK ] MsdMolTest.diffMolMassWeighted (4098 ms)
30: [ RUN ] MsdMolTest.diffMolNonMassWeighted
30:
30: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.mdp]:
30: For a correct single-point energy evaluation with nsteps = 0, use
30: continuation = yes to avoid constraining the input coordinates.
30:
30: Setting the LD random seed to -1711003897
30: Generated 330891 of the 330891 non-bonded parameter combinations
30: Generating 1-4 interactions: fudge = 0.5
30: Generated 330891 of the 330891 1-4 parameter combinations
30: Excluding 2 bonded neighbours molecule type 'SOL'
30: Number of degrees of freedom in T-Coupling group rest is 27.00
30:
30: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.mdp]:
30: NVE simulation with an initial temperature of zero: will use a Verlet
30: buffer of 10%. Check your energy drift!
30:
30:
30: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.mdp]:
30: You are using a plain Coulomb cut-off, which might produce artifacts.
30: You might want to consider using PME electrostatics.
30:
30:
30:
30: There were 3 notes
30: Calculating diffusion coefficients for molecules.
30: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
30: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
30:
30: Select a group to calculate mean squared displacement for:
30: Group 0 ( water) has 15 elements
30: There is one group in the index
30: Split group of 15 atoms into 5 molecules
30: Reading frames from pdb file
Reading frame 0 time 0.000 'water t= 0.00400 step= 20', 15 atoms
30:
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Reading frame 5 time 0.020
Reading frame 6 time 0.024
Reading frame 7 time 0.028
Reading frame 8 time 0.032
Reading frame 9 time 0.036
Reading frame 10 time 0.040
Reading frame 11 time 0.044
Reading frame 12 time 0.048
Reading frame 13 time 0.052
Reading frame 14 time 0.056
Reading frame 15 time 0.060
Reading frame 16 time 0.064
Reading frame 17 time 0.068
Reading frame 18 time 0.072
Reading frame 19 time 0.076
Reading frame 20 time 0.080
30:
30: Used 1 restart points spaced 200 ps over 0.1 ps
30:
30: This run will generate roughly 0 Mb of data
30: <D> = 6.4731 Std. Dev. = 8.0969 Error = 3.6210
30: Fitting from 0.008 to 0.088 ps
30:
30: D[ water] 6.5741 (+/- 0.7753) 1e-5 cm^2/s
30: [ OK ] MsdMolTest.diffMolNonMassWeighted (4101 ms)
30: [ RUN ] MsdMolTest.diffMolSelected
30:
30: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.mdp]:
30: For a correct single-point energy evaluation with nsteps = 0, use
30: continuation = yes to avoid constraining the input coordinates.
30:
30: Setting the LD random seed to 661091925
30: Generated 330891 of the 330891 non-bonded parameter combinations
30: Generating 1-4 interactions: fudge = 0.5
30: Generated 330891 of the 330891 1-4 parameter combinations
30: Excluding 2 bonded neighbours molecule type 'SOL'
30: Number of degrees of freedom in T-Coupling group rest is 27.00
30:
30: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.mdp]:
30: NVE simulation with an initial temperature of zero: will use a Verlet
30: buffer of 10%. Check your energy drift!
30:
30:
30: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.mdp]:
30: You are using a plain Coulomb cut-off, which might produce artifacts.
30: You might want to consider using PME electrostatics.
30:
30:
30:
30: There were 3 notes
30: Calculating diffusion coefficients for molecules.
30: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
30: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
30:
30: Select a group to calculate mean squared displacement for:
30: Group 0 ( mol) has 9 elements
30: There is one group in the index
30: Split group of 9 atoms into 3 molecules
30: Reading frames from pdb file
Reading frame 0 time 0.000 'water t= 0.00400 step= 20', 15 atoms
30:
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Reading frame 5 time 0.020
Reading frame 6 time 0.024
Reading frame 7 time 0.028
Reading frame 8 time 0.032
Reading frame 9 time 0.036
Reading frame 10 time 0.040
Reading frame 11 time 0.044
Reading frame 12 time 0.048
Reading frame 13 time 0.052
Reading frame 14 time 0.056
Reading frame 15 time 0.060
Reading frame 16 time 0.064
Reading frame 17 time 0.068
Reading frame 18 time 0.072
Reading frame 19 time 0.076
Reading frame 20 time 0.080
30:
30: Used 1 restart points spaced 200 ps over 0.1 ps
30:
30: This run will generate roughly 0 Mb of data
30: <D> = 7.3593 Std. Dev. = 9.7910 Error = 5.6529
30: Fitting from 0.008 to 0.088 ps
30:
30: D[ mol] 7.8614 (+/- 1.5619) 1e-5 cm^2/s
30: [ OK ] MsdMolTest.diffMolSelected (4365 ms)
30: [----------] 3 tests from MsdMolTest (12566 ms total)
30:
30: [----------] 6 tests from NoFatalErrorWhenWritingFrom/GmxTraj
30: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0
30: Group 0 ( System) has 6 elements
30: Group 1 ( Water) has 6 elements
30: Group 2 ( SOL) has 6 elements
30: Select a group: trr version: GMX_trn_file (single precision)
30:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
30: Selected 0: 'System'
30: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 (8 ms)
30: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1
30: Group 0 ( System) has 6 elements
30: Group 1 ( Water) has 6 elements
30: Group 2 ( SOL) has 6 elements
30: Select a group:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
30: Selected 0: 'System'
30: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 (12 ms)
30: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2
30: Group 0 ( System) has 6 elements
30: Group 1 ( Water) has 6 elements
30: Group 2 ( SOL) has 6 elements
30: Select a group:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
30: Selected 0: 'System'
30: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 (9 ms)
30: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3
30: Group 0 ( System) has 6 elements
30: Group 1 ( Water) has 6 elements
30: Group 2 ( SOL) has 6 elements
30: Select a group: Reading frames from gro file '', 6 atoms.
30:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
30: Selected 0: 'System'
30: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 (9 ms)
30: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4
30: Group 0 ( System) has 6 elements
30: Group 1 ( Water) has 6 elements
30: Group 2 ( SOL) has 6 elements
30: Select a group: Reading frames from pdb file
Reading frame 0 time 0.000 't= 0.00000', 6 atoms
30:
Reading frame 1 time 0.000
Last frame 1 time 0.000
30: Selected 0: 'System'
30: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 (8 ms)
30: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5
30: Group 0 ( System) has 6 elements
30: Group 1 ( Water) has 6 elements
30: Group 2 ( SOL) has 6 elements
30: Select a group:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
30: Selected 0: 'System'
30: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 (9 ms)
30: [----------] 6 tests from NoFatalErrorWhenWritingFrom/GmxTraj (55 ms total)
30:
30: [----------] Global test environment tear-down
30: [==========] 27 tests from 5 test cases ran. (12692 ms total)
30: [ PASSED ] 27 tests.
30/52 Test #30: GmxAnaTest .......................... Passed 12.77 sec
test 31
Start 31: GmxPreprocessTests
31: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/gmxpreprocess-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/GmxPreprocessTests.xml"
31: Test timeout computed to be: 30
31: [==========] Running 51 tests from 9 test cases.
31: [----------] Global test environment set-up.
31: [----------] 4 tests from GenconfTest
31: [ RUN ] GenconfTest.nbox_Works
31: [ OK ] GenconfTest.nbox_Works (5 ms)
31: [ RUN ] GenconfTest.nbox_norenumber_Works
31: [ OK ] GenconfTest.nbox_norenumber_Works (3 ms)
31: [ RUN ] GenconfTest.nbox_dist_Works
31: [ OK ] GenconfTest.nbox_dist_Works (4 ms)
31: [ RUN ] GenconfTest.nbox_rot_Works
31: center of geometry: 1.733667, 1.477000, 0.905167
31: center of geometry: 1.733667, 1.477000, 0.905167
31: center of geometry: 1.733667, 1.477000, 0.905167
31: center of geometry: 1.733667, 1.477000, 0.905167
31: center of geometry: 1.733667, 1.477000, 0.905167
31: center of geometry: 1.733667, 1.477000, 0.905167
31: center of geometry: 1.733667, 1.477000, 0.905167
31: center of geometry: 1.733667, 1.477000, 0.905167
31: center of geometry: 1.733667, 1.477000, 0.905167
31: center of geometry: 1.733667, 1.477000, 0.905167
31: center of geometry: 1.733667, 1.477000, 0.905167
31: center of geometry: 1.733667, 1.477000, 0.905167
31: [ OK ] GenconfTest.nbox_rot_Works (4 ms)
31: [----------] 4 tests from GenconfTest (16 ms total)
31:
31: [----------] 2 tests from GenionTest
31: [ RUN ] GenionTest.HighConcentrationIonPlacement
31:
31: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]:
31: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet
31: buffer. The cluster pair list does have a buffering effect, but choosing
31: a larger rlist might be necessary for good energy conservation.
31:
31:
31: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]:
31: For a correct single-point energy evaluation with nsteps = 0, use
31: continuation = yes to avoid constraining the input coordinates.
31:
31: Setting the LD random seed to -1276786639
31: Generated 331705 of the 331705 non-bonded parameter combinations
31: Generating 1-4 interactions: fudge = 0.5
31: Generated 331705 of the 331705 1-4 parameter combinations
31: Excluding 2 bonded neighbours molecule type 'SOL'
31: Excluding 3 bonded neighbours molecule type 'methane'
31: Number of degrees of freedom in T-Coupling group rest is 1308.00
31:
31: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]:
31: You are using a plain Coulomb cut-off, which might produce artifacts.
31: You might want to consider using PME electrostatics.
31:
31:
31:
31: There were 3 notes
31: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
31: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
31: Group 0 ( System) has 653 elements
31: Group 1 ( Water) has 648 elements
31: Group 2 ( SOL) has 648 elements
31: Group 3 ( non-Water) has 5 elements
31: Group 4 ( Other) has 5 elements
31: Group 5 ( METH) has 5 elements
31: Select a group: Number of (3-atomic) solvent molecules: 216
31: Using random seed 1997.
31: Replacing solvent molecule 56 (atom 168) with NA
31: Replacing solvent molecule 120 (atom 360) with NA
31: Replacing solvent molecule 182 (atom 546) with NA
31: Replacing solvent molecule 71 (atom 213) with NA
31: Replacing solvent molecule 189 (atom 567) with CL
31: Replacing solvent molecule 54 (atom 162) with CL
31: Replacing solvent molecule 155 (atom 465) with CL
31: Replacing solvent molecule 99 (atom 297) with CL
31:
31: Analysing residue names:
31: There are: 216 Water residues
31: There are: 1 Other residues
31: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
31: This run will generate roughly 0 Mb of data
31: Will try to add 4 NA ions and 4 CL ions.
31: Select a continuous group of solvent molecules
31: Selected 1: 'Water'
31: [ OK ] GenionTest.HighConcentrationIonPlacement (4307 ms)
31: [ RUN ] GenionTest.NoIonPlacement
31:
31: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]:
31: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet
31: buffer. The cluster pair list does have a buffering effect, but choosing
31: a larger rlist might be necessary for good energy conservation.
31:
31:
31: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]:
31: For a correct single-point energy evaluation with nsteps = 0, use
31: continuation = yes to avoid constraining the input coordinates.
31:
31: Setting the LD random seed to -1835386184
31: Generated 331705 of the 331705 non-bonded parameter combinations
31: Generating 1-4 interactions: fudge = 0.5
31: Generated 331705 of the 331705 1-4 parameter combinations
31: Excluding 2 bonded neighbours molecule type 'SOL'
31: Excluding 3 bonded neighbours molecule type 'methane'
31: Number of degrees of freedom in T-Coupling group rest is 1308.00
31:
31: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]:
31: You are using a plain Coulomb cut-off, which might produce artifacts.
31: You might want to consider using PME electrostatics.
31:
31:
31:
31: There were 3 notes
31: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
31: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
31: No ions to add, will just copy input configuration.
31: Analysing residue names:
31: There are: 216 Water residues
31: There are: 1 Other residues
31: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
31: This run will generate roughly 0 Mb of data
31: [ OK ] GenionTest.NoIonPlacement (4323 ms)
31: [----------] 2 tests from GenionTest (8631 ms total)
31:
31: [----------] 1 test from GenRestrTest
31: [ RUN ] GenRestrTest.SimpleRestraintsGenerated
31:
31: Reading structure file
31: Group 0 ( System) has 156 elements
31: Group 1 ( Protein) has 156 elements
31: Group 2 ( Protein-H) has 75 elements
31: Group 3 ( C-alpha) has 10 elements
31: Group 4 ( Backbone) has 30 elements
31: Group 5 ( MainChain) has 40 elements
31: Group 6 ( MainChain+Cb) has 49 elements
31: Group 7 ( MainChain+H) has 52 elements
31: Group 8 ( SideChain) has 104 elements
31: Group 9 ( SideChain-H) has 35 elements
31: Select a group: Select group to position restrain
31: Selected 3: 'C-alpha'
31: [ OK ] GenRestrTest.SimpleRestraintsGenerated (14 ms)
31: [----------] 1 test from GenRestrTest (15 ms total)
31:
31: [----------] 9 tests from PreprocessingAtomTypesTest
31: [ RUN ] PreprocessingAtomTypesTest.EmptyOnCreate
31: [ OK ] PreprocessingAtomTypesTest.EmptyOnCreate (0 ms)
31: [ RUN ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid
31: [ OK ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid (0 ms)
31: [ RUN ] PreprocessingAtomTypesTest.AddTypeWorks
31: [ OK ] PreprocessingAtomTypesTest.AddTypeWorks (0 ms)
31: [ RUN ] PreprocessingAtomTypesTest.AddMultipleTypesWorks
31: [ OK ] PreprocessingAtomTypesTest.AddMultipleTypesWorks (0 ms)
31: [ RUN ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry
31: [ OK ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry (0 ms)
31: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFound
31: [ OK ] PreprocessingAtomTypesTest.CorrectNameFound (0 ms)
31: [ RUN ] PreprocessingAtomTypesTest.WrongNameNotFound
31: [ OK ] PreprocessingAtomTypesTest.WrongNameNotFound (0 ms)
31: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber
31: [ OK ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber (0 ms)
31: [ RUN ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber
31: [ OK ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber (0 ms)
31: [----------] 9 tests from PreprocessingAtomTypesTest (0 ms total)
31:
31: [----------] 10 tests from PreprocessingBondAtomTypeTest
31: [ RUN ] PreprocessingBondAtomTypeTest.EmptyOnCreate
31: [ OK ] PreprocessingBondAtomTypeTest.EmptyOnCreate (0 ms)
31: [ RUN ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid
31: [ OK ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid (0 ms)
31: [ RUN ] PreprocessingBondAtomTypeTest.AddTypeWorks
31: [ OK ] PreprocessingBondAtomTypeTest.AddTypeWorks (0 ms)
31: [ RUN ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks
31: [ OK ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks (0 ms)
31: [ RUN ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry
31: [ OK ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry (1 ms)
31: [ RUN ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType
31: [ OK ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType (0 ms)
31: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFound
31: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFound (0 ms)
31: [ RUN ] PreprocessingBondAtomTypeTest.WrongNameNotFound
31: [ OK ] PreprocessingBondAtomTypeTest.WrongNameNotFound (0 ms)
31: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber
31: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber (0 ms)
31: [ RUN ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber
31: [ OK ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber (0 ms)
31: [----------] 10 tests from PreprocessingBondAtomTypeTest (1 ms total)
31:
31: [----------] 5 tests from InsertMoleculesTest
31: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration
31: Reading solute configuration
31: Initialising inter-atomic distances...
31:
31: WARNING: Masses and atomic (Van der Waals) radii will be guessed
31: based on residue and atom names, since they could not be
31: definitively assigned from the information in your input
31: files. These guessed numbers might deviate from the mass
31: and radius of the atom type. Please check the output
31: files if necessary.
31:
31: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
31: from the source below. This means the results may be different
31: compared to previous GROMACS versions.
31:
31: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
31: A. Bondi
31: van der Waals Volumes and Radii
31: J. Phys. Chem. 68 (1964) pp. 441-451
31: -------- -------- --- Thank You --- -------- --------
31:
31: Using random seed 1997
31:
Try 1 success (now 8 atoms)!
31:
31: Added 1 molecules (out of 1 requested)
31: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoExistingConfiguration_out.gro
31:
31: Output configuration contains 8 atoms in 4 residues
31: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration (26 ms)
31: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox
31: Initialising inter-atomic distances...
31:
31: WARNING: Masses and atomic (Van der Waals) radii will be guessed
31: based on residue and atom names, since they could not be
31: definitively assigned from the information in your input
31: files. These guessed numbers might deviate from the mass
31: and radius of the atom type. Please check the output
31: files if necessary.
31:
31: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
31: from the source below. This means the results may be different
31: compared to previous GROMACS versions.
31:
31: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
31: A. Bondi
31: van der Waals Volumes and Radii
31: J. Phys. Chem. 68 (1964) pp. 441-451
31: -------- -------- --- Thank You --- -------- --------
31:
31: Using random seed 1997
31:
Try 1 success (now 2 atoms)!
31:
Try 2 success (now 4 atoms)!
31:
Try 3 success (now 6 atoms)!
31:
Try 4 success (now 8 atoms)!
31:
Try 5 success (now 10 atoms)!
31:
31: Added 5 molecules (out of 5 requested)
31: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEmptyBox_out.gro
31:
31: Output configuration contains 10 atoms in 10 residues
31: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox (8 ms)
31: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox
31: Reading solute configuration
31: Initialising inter-atomic distances...
31:
31: WARNING: Masses and atomic (Van der Waals) radii will be guessed
31: based on residue and atom names, since they could not be
31: definitively assigned from the information in your input
31: files. These guessed numbers might deviate from the mass
31: and radius of the atom type. Please check the output
31: files if necessary.
31:
31: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
31: from the source below. This means the results may be different
31: compared to previous GROMACS versions.
31:
31: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
31: A. Bondi
31: van der Waals Volumes and Radii
31: J. Phys. Chem. 68 (1964) pp. 441-451
31: -------- -------- --- Thank You --- -------- --------
31:
31: Using random seed 1997
31:
Try 1 success (now 8 atoms)!
31:
Try 2 success (now 10 atoms)!
31:
31: Added 2 molecules (out of 2 requested)
31: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEnlargedBox_out.gro
31:
31: Output configuration contains 10 atoms in 4 residues
31: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox (9 ms)
31: [ RUN ] InsertMoleculesTest.InsertsMoleculesWithReplacement
31: Reading solute configuration
31: Initialising inter-atomic distances...
31:
31: WARNING: Masses and atomic (Van der Waals) radii will be guessed
31: based on residue and atom names, since they could not be
31: definitively assigned from the information in your input
31: files. These guessed numbers might deviate from the mass
31: and radius of the atom type. Please check the output
31: files if necessary.
31:
31: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
31: from the source below. This means the results may be different
31: compared to previous GROMACS versions.
31:
31: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
31: A. Bondi
31: van der Waals Volumes and Radii
31: J. Phys. Chem. 68 (1964) pp. 441-451
31: -------- -------- --- Thank You --- -------- --------
31:
31: Using random seed 1997
31:
Try 1 success (now 650 atoms)!
31:
Try 2 success (now 652 atoms)!
31:
Try 3 success (now 654 atoms)!
31:
Try 4 success (now 656 atoms)!
31:
31: Added 4 molecules (out of 4 requested)
31: Replaced 8 residues (24 atoms)
31: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesWithReplacement_out.gro
31:
31: Output configuration contains 632 atoms in 212 residues
31: [ OK ] InsertMoleculesTest.InsertsMoleculesWithReplacement (43 ms)
31: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions
31: Initialising inter-atomic distances...
31:
31: WARNING: Masses and atomic (Van der Waals) radii will be guessed
31: based on residue and atom names, since they could not be
31: definitively assigned from the information in your input
31: files. These guessed numbers might deviate from the mass
31: and radius of the atom type. Please check the output
31: files if necessary.
31:
31: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
31: from the source below. This means the results may be different
31: compared to previous GROMACS versions.
31:
31: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
31: A. Bondi
31: van der Waals Volumes and Radii
31: J. Phys. Chem. 68 (1964) pp. 441-451
31: -------- -------- --- Thank You --- -------- --------
31:
31: Using random seed 1997
31: Read 4 positions from file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_5.dat
31:
31:
Try 1 success (now 2 atoms)!
31:
Try 2 success (now 4 atoms)!
31:
Try 3
Try 4
Try 5
Try 6
Try 7
Try 8
Try 9
Try 10
Try 11
Try 12 skipped position (0.990, 2.010, 3.000)
31:
Try 13 success (now 6 atoms)!
31:
31: Added 3 molecules (out of 4 requested)
31: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_out.gro
31:
31: Output configuration contains 6 atoms in 3 residues
31: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions (9 ms)
31: [----------] 5 tests from InsertMoleculesTest (95 ms total)
31:
31: [----------] 14 tests from GetIrTest
31: [ RUN ] GetIrTest.HandlesDifferentKindsOfMdpLines
31: Ignoring obsolete mdp entry 'title'
31: Replacing old mdp entry 'xtc_grps' by 'compressed-x-grps'
31:
31: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_HandlesDifferentKindsOfMdpLines_input.mdp]:
31: For a correct single-point energy evaluation with nsteps = 0, use
31: continuation = yes to avoid constraining the input coordinates.
31:
31: [ OK ] GetIrTest.HandlesDifferentKindsOfMdpLines (31 ms)
31: [ RUN ] GetIrTest.RejectsNonCommentLineWithNoEquals
31: [ OK ] GetIrTest.RejectsNonCommentLineWithNoEquals (36 ms)
31: [ RUN ] GetIrTest.AcceptsKeyWithoutValue
31:
31: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsKeyWithoutValue_input.mdp]:
31: For a correct single-point energy evaluation with nsteps = 0, use
31: continuation = yes to avoid constraining the input coordinates.
31:
31: [ OK ] GetIrTest.AcceptsKeyWithoutValue (27 ms)
31: [ RUN ] GetIrTest.RejectsValueWithoutKey
31: [ OK ] GetIrTest.RejectsValueWithoutKey (34 ms)
31: [ RUN ] GetIrTest.RejectsEmptyKeyAndEmptyValue
31: [ OK ] GetIrTest.RejectsEmptyKeyAndEmptyValue (30 ms)
31: [ RUN ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment
31:
31: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsDefineParametersWithValuesIncludingAssignment_input.mdp]:
31: For a correct single-point energy evaluation with nsteps = 0, use
31: continuation = yes to avoid constraining the input coordinates.
31:
31: [ OK ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment (17 ms)
31: [ RUN ] GetIrTest.AcceptsEmptyLines
31:
31: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsEmptyLines_input.mdp]:
31: For a correct single-point energy evaluation with nsteps = 0, use
31: continuation = yes to avoid constraining the input coordinates.
31:
31: [ OK ] GetIrTest.AcceptsEmptyLines (18 ms)
31: [ RUN ] GetIrTest.AcceptsElectricField
31:
31: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricField_input.mdp]:
31: For a correct single-point energy evaluation with nsteps = 0, use
31: continuation = yes to avoid constraining the input coordinates.
31:
31: [ OK ] GetIrTest.AcceptsElectricField (21 ms)
31: [ RUN ] GetIrTest.AcceptsElectricFieldPulsed
31:
31: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldPulsed_input.mdp]:
31: For a correct single-point energy evaluation with nsteps = 0, use
31: continuation = yes to avoid constraining the input coordinates.
31:
31: [ OK ] GetIrTest.AcceptsElectricFieldPulsed (22 ms)
31: [ RUN ] GetIrTest.AcceptsElectricFieldOscillating
31:
31: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldOscillating_input.mdp]:
31: For a correct single-point energy evaluation with nsteps = 0, use
31: continuation = yes to avoid constraining the input coordinates.
31:
31: [ OK ] GetIrTest.AcceptsElectricFieldOscillating (19 ms)
31: [ RUN ] GetIrTest.RejectsDuplicateOldAndNewKeys
31: [ OK ] GetIrTest.RejectsDuplicateOldAndNewKeys (13 ms)
31: [ RUN ] GetIrTest.AcceptsImplicitSolventNo
31:
31: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsImplicitSolventNo_input.mdp]:
31: For a correct single-point energy evaluation with nsteps = 0, use
31: continuation = yes to avoid constraining the input coordinates.
31:
31: [ OK ] GetIrTest.AcceptsImplicitSolventNo (17 ms)
31: [ RUN ] GetIrTest.RejectsImplicitSolventYes
31: [ OK ] GetIrTest.RejectsImplicitSolventYes (30 ms)
31: [ RUN ] GetIrTest.AcceptsMimic
31:
31: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsMimic_input.mdp]:
31: For a correct single-point energy evaluation with nsteps = 0, use
31: continuation = yes to avoid constraining the input coordinates.
31:
31: [ OK ] GetIrTest.AcceptsMimic (18 ms)
31: [----------] 14 tests from GetIrTest (333 ms total)
31:
31: [----------] 5 tests from SolvateTest
31: [ RUN ] SolvateTest.cs_box_Works
31: Reading solvent configuration
31:
31: Initialising inter-atomic distances...
31:
31: WARNING: Masses and atomic (Van der Waals) radii will be guessed
31: based on residue and atom names, since they could not be
31: definitively assigned from the information in your input
31: files. These guessed numbers might deviate from the mass
31: and radius of the atom type. Please check the output
31: files if necessary.
31:
31: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
31: from the source below. This means the results may be different
31: compared to previous GROMACS versions.
31:
31: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
31: A. Bondi
31: van der Waals Volumes and Radii
31: J. Phys. Chem. 68 (1964) pp. 441-451
31: -------- -------- --- Thank You --- -------- --------
31:
31: Generating solvent configuration
31: Will generate new solvent configuration of 1x1x1 boxes
31: Solvent box contains 270 atoms in 90 residues
31: Removed 129 solvent atoms due to solvent-solvent overlap
31: Sorting configuration
31: Found 1 molecule type:
31: SOL ( 3 atoms): 47 residues
31: Generated solvent containing 141 atoms in 47 residues
31: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_box_Works_out.gro
31:
31: Output configuration contains 141 atoms in 47 residues
31: Volume : 1.331 (nm^3)
31: Density : 1056.36 (g/l)
31: Number of solvent molecules: 47
31:
31: [ OK ] SolvateTest.cs_box_Works (53 ms)
31: [ RUN ] SolvateTest.cs_cp_Works
31: Reading solute configuration
31: Reading solvent configuration
31:
31: Initialising inter-atomic distances...
31:
31: WARNING: Masses and atomic (Van der Waals) radii will be guessed
31: based on residue and atom names, since they could not be
31: definitively assigned from the information in your input
31: files. These guessed numbers might deviate from the mass
31: and radius of the atom type. Please check the output
31: files if necessary.
31:
31: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
31: from the source below. This means the results may be different
31: compared to previous GROMACS versions.
31:
31: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
31: A. Bondi
31: van der Waals Volumes and Radii
31: J. Phys. Chem. 68 (1964) pp. 441-451
31: -------- -------- --- Thank You --- -------- --------
31:
31: Generating solvent configuration
31: Will generate new solvent configuration of 2x2x2 boxes
31: Solvent box contains 3660 atoms in 1220 residues
31: Removed 987 solvent atoms due to solvent-solvent overlap
31: Removed 15 solvent atoms due to solute-solvent overlap
31: Sorting configuration
31: Found 1 molecule type:
31: SOL ( 3 atoms): 886 residues
31: Generated solvent containing 2658 atoms in 886 residues
31: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_Works_out.gro
31:
31: Output configuration contains 2664 atoms in 888 residues
31: Volume : 27.2709 (nm^3)
31: Density : 974.777 (g/l)
31: Number of solvent molecules: 886
31:
31: [ OK ] SolvateTest.cs_cp_Works (279 ms)
31: [ RUN ] SolvateTest.cs_cp_p_Works
31: Reading solute configuration
31: Reading solvent configuration
31:
31: Initialising inter-atomic distances...
31:
31: WARNING: Masses and atomic (Van der Waals) radii will be guessed
31: based on residue and atom names, since they could not be
31: definitively assigned from the information in your input
31: files. These guessed numbers might deviate from the mass
31: and radius of the atom type. Please check the output
31: files if necessary.
31:
31: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
31: from the source below. This means the results may be different
31: compared to previous GROMACS versions.
31:
31: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
31: A. Bondi
31: van der Waals Volumes and Radii
31: J. Phys. Chem. 68 (1964) pp. 441-451
31: -------- -------- --- Thank You --- -------- --------
31:
31: Generating solvent configuration
31: Will generate new solvent configuration of 2x2x2 boxes
31: Solvent box contains 3660 atoms in 1220 residues
31: Removed 987 solvent atoms due to solvent-solvent overlap
31: Removed 15 solvent atoms due to solute-solvent overlap
31: Sorting configuration
31: Found 1 molecule type:
31: SOL ( 3 atoms): 886 residues
31: Generated solvent containing 2658 atoms in 886 residues
31: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_out.gro
31:
31: Output configuration contains 2664 atoms in 888 residues
31: Volume : 27.2709 (nm^3)
31: Density : 974.777 (g/l)
31: Number of solvent molecules: 886
31:
31: Processing topology
31: Adding line for 886 solvent molecules with resname (SOL) to topology file (/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_spc-and-methanol.top)
31: [ OK ] SolvateTest.cs_cp_p_Works (284 ms)
31: [ RUN ] SolvateTest.shell_Works
31: Reading solute configuration
31: Reading solvent configuration
31:
31: Initialising inter-atomic distances...
31:
31: WARNING: Masses and atomic (Van der Waals) radii will be guessed
31: based on residue and atom names, since they could not be
31: definitively assigned from the information in your input
31: files. These guessed numbers might deviate from the mass
31: and radius of the atom type. Please check the output
31: files if necessary.
31:
31: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
31: from the source below. This means the results may be different
31: compared to previous GROMACS versions.
31:
31: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
31: A. Bondi
31: van der Waals Volumes and Radii
31: J. Phys. Chem. 68 (1964) pp. 441-451
31: -------- -------- --- Thank You --- -------- --------
31:
31: Generating solvent configuration
31: Will generate new solvent configuration of 2x2x2 boxes
31: Solvent box contains 3660 atoms in 1220 residues
31: Removed 987 solvent atoms due to solvent-solvent overlap
31: Removed 1902 solvent atoms more than 1.000000 nm from solute.
31: Removed 15 solvent atoms due to solute-solvent overlap
31: Sorting configuration
31: Found 1 molecule type:
31: SOL ( 3 atoms): 252 residues
31: Generated solvent containing 756 atoms in 252 residues
31: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_shell_Works_out.gro
31:
31: Output configuration contains 762 atoms in 254 residues
31: Volume : 27.2709 (nm^3)
31: Density : 279.3 (g/l)
31: Number of solvent molecules: 252
31:
31: [ OK ] SolvateTest.shell_Works (163 ms)
31: [ RUN ] SolvateTest.update_Topology_Works
31: Reading solute configuration
31: Reading solvent configuration
31:
31: Initialising inter-atomic distances...
31:
31: WARNING: Masses and atomic (Van der Waals) radii will be guessed
31: based on residue and atom names, since they could not be
31: definitively assigned from the information in your input
31: files. These guessed numbers might deviate from the mass
31: and radius of the atom type. Please check the output
31: files if necessary.
31:
31: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
31: from the source below. This means the results may be different
31: compared to previous GROMACS versions.
31:
31: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
31: A. Bondi
31: van der Waals Volumes and Radii
31: J. Phys. Chem. 68 (1964) pp. 441-451
31: -------- -------- --- Thank You --- -------- --------
31:
31: Generating solvent configuration
31: Will generate new solvent configuration of 3x3x3 boxes
31: Solvent box contains 14952 atoms in 4984 residues
31: Removed 2787 solvent atoms due to solvent-solvent overlap
31: Removed 30 solvent atoms due to solute-solvent overlap
31: Sorting configuration
31: Found 2 different molecule types:
31: HOH ( 3 atoms): 1876 residues
31: SOL ( 3 atoms): 2169 residues
31: Generated solvent containing 0 atoms in 0 residues
31: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_out.gro
31:
31: Output configuration contains 12141 atoms in 4047 residues
31: Volume : 125 (nm^3)
31: Density : 968.963 (g/l)
31: Number of solvent molecules: 4045
31:
31: Processing topology
31: Adding line for 1876 solvent molecules with resname (HOH) to topology file (/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top)
31: Adding line for 2169 solvent molecules with resname (SOL) to topology file (/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top)
31: [ OK ] SolvateTest.update_Topology_Works (1201 ms)
31: [----------] 5 tests from SolvateTest (1980 ms total)
31:
31: [----------] 1 test from TopDirTests
31: [ RUN ] TopDirTests.NamesArrayHasCorrectSize
31: [ OK ] TopDirTests.NamesArrayHasCorrectSize (0 ms)
31: [----------] 1 test from TopDirTests (0 ms total)
31:
31: [----------] Global test environment tear-down
31: [==========] 51 tests from 9 test cases ran. (11074 ms total)
31: [ PASSED ] 51 tests.
31/52 Test #31: GmxPreprocessTests .................. Passed 11.15 sec
test 32
Start 32: Pdb2gmx1Test
32: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/pdb2gmx1-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/Pdb2gmx1Test.xml"
32: Test timeout computed to be: 30
32: [==========] Running 24 tests from 1 test case.
32: [----------] Global test environment set-up.
32: [----------] 24 tests from ForOplsaa/Pdb2gmxTest
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/0
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 25 donors and 23 acceptors were found.
32: There are 41 hydrogen bonds
32: Will use HISE for residue 8
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS3 HIS8
32: SG9 NE251
32: HIS8 NE251 1.055
32: MET12 SD83 0.763 0.990
32: Making bonds...
32: Number of bonds was 254, now 254
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 653 pairs
32: Before cleaning: 663 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 663 dihedrals, 51 impropers, 457 angles
32: 650 pairs, 254 bonds and 0 virtual sites
32: Total mass 1846.112 a.m.u.
32: Total charge 0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 128
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (128 atoms, 16 residues)
32: Identified residue ALA2 as a starting terminus.
32: Identified residue SER17 as a ending terminus.
32: Start terminus ALA-2: NH3+
32: End terminus SER-17: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 252 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
32: The Oplsaa force field and the tip3p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/0 (516 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/1
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 30 donors and 22 acceptors were found.
32: There are 36 hydrogen bonds
32: Will use HISE for residue 29
32: Will use HISE for residue 32
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS27 HIS29
32: SG90 NE2111
32: HIS29 NE2111 0.987
32: HIS32 NE2135 1.590 1.155
32: Making bonds...
32: Number of bonds was 290, now 290
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 748 pairs
32: Before cleaning: 778 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 778 dihedrals, 72 impropers, 516 angles
32: 736 pairs, 290 bonds and 0 virtual sites
32: Total mass 2088.357 a.m.u.
32: Total charge 1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 149
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (149 atoms, 16 residues)
32: Identified residue THR18 as a starting terminus.
32: Identified residue PHE33 as a ending terminus.
32: Start terminus THR-18: NH3+
32: End terminus PHE-33: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 281 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
32: The Oplsaa force field and the tip3p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/1 (554 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/2
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 22 acceptors were found.
32: There are 26 hydrogen bonds
32: Will use HISE for residue 45
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS45
32: NE295
32: MET46 SD102 1.078
32: Making bonds...
32: Number of bonds was 261, now 261
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 676 pairs
32: Before cleaning: 696 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 696 dihedrals, 56 impropers, 472 angles
32: 667 pairs, 261 bonds and 0 virtual sites
32: Total mass 1861.128 a.m.u.
32: Total charge -1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 132
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (132 atoms, 16 residues)
32: Identified residue ALA34 as a starting terminus.
32: Identified residue ALA49 as a ending terminus.
32: Start terminus ALA-34: NH3+
32: End terminus ALA-49: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 255 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
32: The Oplsaa force field and the tip3p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/2 (510 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/3
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 21 acceptors were found.
32: There are 30 hydrogen bonds
32: Will use HISE for residue 60
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS60
32: NE285
32: CYS62 SG98 0.803
32: Making bonds...
32: Number of bonds was 232, now 232
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 603 pairs
32: Before cleaning: 618 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 618 dihedrals, 48 impropers, 419 angles
32: 597 pairs, 232 bonds and 0 virtual sites
32: Total mass 1662.883 a.m.u.
32: Total charge 0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 117
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (117 atoms, 16 residues)
32: Identified residue LYS50 as a starting terminus.
32: Identified residue PRO65 as a ending terminus.
32: Start terminus LYS-50: NH3+
32: End terminus PRO-65: PRO-COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 228 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
32: The Oplsaa force field and the tip3p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/3 (466 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/4
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 25 donors and 23 acceptors were found.
32: There are 41 hydrogen bonds
32: Will use HISE for residue 8
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS3 HIS8
32: SG9 NE251
32: HIS8 NE251 1.055
32: MET12 SD83 0.763 0.990
32: Making bonds...
32: Number of bonds was 254, now 254
32: Marked 124 virtual sites
32: Added 16 dummy masses
32: Added 26 new constraints
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 653 pairs
32: Before cleaning: 663 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 663 dihedrals, 51 impropers, 457 angles
32: 650 pairs, 254 bonds and 130 virtual sites
32: Total mass 1846.112 a.m.u.
32: Total charge 0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 128
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (128 atoms, 16 residues)
32: Identified residue ALA2 as a starting terminus.
32: Identified residue SER17 as a ending terminus.
32: Start terminus ALA-2: NH3+
32: End terminus SER-17: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 252 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
32: The Oplsaa force field and the tip3p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/4 (539 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/5
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 30 donors and 22 acceptors were found.
32: There are 36 hydrogen bonds
32: Will use HISE for residue 29
32: Will use HISE for residue 32
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS27 HIS29
32: SG90 NE2111
32: HIS29 NE2111 0.987
32: HIS32 NE2135 1.590 1.155
32: Making bonds...
32: Number of bonds was 290, now 290
32: Marked 132 virtual sites
32: Added 10 dummy masses
32: Added 19 new constraints
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 748 pairs
32: Before cleaning: 778 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 778 dihedrals, 72 impropers, 516 angles
32: 736 pairs, 290 bonds and 133 virtual sites
32: Total mass 2088.357 a.m.u.
32: Total charge 1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 149
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (149 atoms, 16 residues)
32: Identified residue THR18 as a starting terminus.
32: Identified residue PHE33 as a ending terminus.
32: Start terminus THR-18: NH3+
32: End terminus PHE-33: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 281 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
32: The Oplsaa force field and the tip3p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/5 (587 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/6
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 22 acceptors were found.
32: There are 26 hydrogen bonds
32: Will use HISE for residue 45
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS45
32: NE295
32: MET46 SD102 1.078
32: Making bonds...
32: Number of bonds was 261, now 261
32: Marked 123 virtual sites
32: Added 22 dummy masses
32: Added 35 new constraints
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 676 pairs
32: Before cleaning: 696 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 696 dihedrals, 56 impropers, 472 angles
32: 667 pairs, 261 bonds and 132 virtual sites
32: Total mass 1861.128 a.m.u.
32: Total charge -1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 132
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (132 atoms, 16 residues)
32: Identified residue ALA34 as a starting terminus.
32: Identified residue ALA49 as a ending terminus.
32: Start terminus ALA-34: NH3+
32: End terminus ALA-49: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 255 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
32: The Oplsaa force field and the tip3p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/6 (562 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/7
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 21 acceptors were found.
32: There are 30 hydrogen bonds
32: Will use HISE for residue 60
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS60
32: NE285
32: CYS62 SG98 0.803
32: Making bonds...
32: Number of bonds was 232, now 232
32: Marked 111 virtual sites
32: Added 18 dummy masses
32: Added 31 new constraints
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 603 pairs
32: Before cleaning: 618 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 618 dihedrals, 48 impropers, 419 angles
32: 597 pairs, 232 bonds and 116 virtual sites
32: Total mass 1662.883 a.m.u.
32: Total charge 0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 117
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (117 atoms, 16 residues)
32: Identified residue LYS50 as a starting terminus.
32: Identified residue PRO65 as a ending terminus.
32: Start terminus LYS-50: NH3+
32: End terminus PRO-65: PRO-COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 228 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
32: The Oplsaa force field and the tip3p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/7 (503 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/8
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 25 donors and 23 acceptors were found.
32: There are 41 hydrogen bonds
32: Will use HISE for residue 8
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS3 HIS8
32: SG9 NE251
32: HIS8 NE251 1.055
32: MET12 SD83 0.763 0.990
32: Making bonds...
32: Number of bonds was 254, now 254
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 653 pairs
32: Before cleaning: 663 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 663 dihedrals, 51 impropers, 457 angles
32: 650 pairs, 254 bonds and 0 virtual sites
32: Total mass 1846.112 a.m.u.
32: Total charge 0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 128
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (128 atoms, 16 residues)
32: Identified residue ALA2 as a starting terminus.
32: Identified residue SER17 as a ending terminus.
32: Start terminus ALA-2: NH3+
32: End terminus SER-17: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 252 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
32: The Oplsaa force field and the tip4p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/8 (501 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/9
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 30 donors and 22 acceptors were found.
32: There are 36 hydrogen bonds
32: Will use HISE for residue 29
32: Will use HISE for residue 32
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS27 HIS29
32: SG90 NE2111
32: HIS29 NE2111 0.987
32: HIS32 NE2135 1.590 1.155
32: Making bonds...
32: Number of bonds was 290, now 290
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 748 pairs
32: Before cleaning: 778 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 778 dihedrals, 72 impropers, 516 angles
32: 736 pairs, 290 bonds and 0 virtual sites
32: Total mass 2088.357 a.m.u.
32: Total charge 1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 149
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (149 atoms, 16 residues)
32: Identified residue THR18 as a starting terminus.
32: Identified residue PHE33 as a ending terminus.
32: Start terminus THR-18: NH3+
32: End terminus PHE-33: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 281 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
32: The Oplsaa force field and the tip4p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/9 (567 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/10
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 22 acceptors were found.
32: There are 26 hydrogen bonds
32: Will use HISE for residue 45
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS45
32: NE295
32: MET46 SD102 1.078
32: Making bonds...
32: Number of bonds was 261, now 261
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 676 pairs
32: Before cleaning: 696 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 696 dihedrals, 56 impropers, 472 angles
32: 667 pairs, 261 bonds and 0 virtual sites
32: Total mass 1861.128 a.m.u.
32: Total charge -1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 132
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (132 atoms, 16 residues)
32: Identified residue ALA34 as a starting terminus.
32: Identified residue ALA49 as a ending terminus.
32: Start terminus ALA-34: NH3+
32: End terminus ALA-49: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 255 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
32: The Oplsaa force field and the tip4p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/10 (509 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/11
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 21 acceptors were found.
32: There are 30 hydrogen bonds
32: Will use HISE for residue 60
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS60
32: NE285
32: CYS62 SG98 0.803
32: Making bonds...
32: Number of bonds was 232, now 232
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 603 pairs
32: Before cleaning: 618 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 618 dihedrals, 48 impropers, 419 angles
32: 597 pairs, 232 bonds and 0 virtual sites
32: Total mass 1662.883 a.m.u.
32: Total charge 0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 117
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (117 atoms, 16 residues)
32: Identified residue LYS50 as a starting terminus.
32: Identified residue PRO65 as a ending terminus.
32: Start terminus LYS-50: NH3+
32: End terminus PRO-65: PRO-COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 228 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
32: The Oplsaa force field and the tip4p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/11 (470 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/12
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 25 donors and 23 acceptors were found.
32: There are 41 hydrogen bonds
32: Will use HISE for residue 8
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS3 HIS8
32: SG9 NE251
32: HIS8 NE251 1.055
32: MET12 SD83 0.763 0.990
32: Making bonds...
32: Number of bonds was 254, now 254
32: Marked 124 virtual sites
32: Added 16 dummy masses
32: Added 26 new constraints
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 653 pairs
32: Before cleaning: 663 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 663 dihedrals, 51 impropers, 457 angles
32: 650 pairs, 254 bonds and 130 virtual sites
32: Total mass 1846.112 a.m.u.
32: Total charge 0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 128
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (128 atoms, 16 residues)
32: Identified residue ALA2 as a starting terminus.
32: Identified residue SER17 as a ending terminus.
32: Start terminus ALA-2: NH3+
32: End terminus SER-17: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 252 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
32: The Oplsaa force field and the tip4p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/12 (535 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/13
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 30 donors and 22 acceptors were found.
32: There are 36 hydrogen bonds
32: Will use HISE for residue 29
32: Will use HISE for residue 32
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS27 HIS29
32: SG90 NE2111
32: HIS29 NE2111 0.987
32: HIS32 NE2135 1.590 1.155
32: Making bonds...
32: Number of bonds was 290, now 290
32: Marked 132 virtual sites
32: Added 10 dummy masses
32: Added 19 new constraints
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 748 pairs
32: Before cleaning: 778 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 778 dihedrals, 72 impropers, 516 angles
32: 736 pairs, 290 bonds and 133 virtual sites
32: Total mass 2088.357 a.m.u.
32: Total charge 1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 149
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (149 atoms, 16 residues)
32: Identified residue THR18 as a starting terminus.
32: Identified residue PHE33 as a ending terminus.
32: Start terminus THR-18: NH3+
32: End terminus PHE-33: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 281 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
32: The Oplsaa force field and the tip4p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/13 (591 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/14
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 22 acceptors were found.
32: There are 26 hydrogen bonds
32: Will use HISE for residue 45
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS45
32: NE295
32: MET46 SD102 1.078
32: Making bonds...
32: Number of bonds was 261, now 261
32: Marked 123 virtual sites
32: Added 22 dummy masses
32: Added 35 new constraints
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 676 pairs
32: Before cleaning: 696 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 696 dihedrals, 56 impropers, 472 angles
32: 667 pairs, 261 bonds and 132 virtual sites
32: Total mass 1861.128 a.m.u.
32: Total charge -1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 132
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (132 atoms, 16 residues)
32: Identified residue ALA34 as a starting terminus.
32: Identified residue ALA49 as a ending terminus.
32: Start terminus ALA-34: NH3+
32: End terminus ALA-49: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 255 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
32: The Oplsaa force field and the tip4p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/14 (559 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/15
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 21 acceptors were found.
32: There are 30 hydrogen bonds
32: Will use HISE for residue 60
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS60
32: NE285
32: CYS62 SG98 0.803
32: Making bonds...
32: Number of bonds was 232, now 232
32: Marked 111 virtual sites
32: Added 18 dummy masses
32: Added 31 new constraints
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 603 pairs
32: Before cleaning: 618 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 618 dihedrals, 48 impropers, 419 angles
32: 597 pairs, 232 bonds and 116 virtual sites
32: Total mass 1662.883 a.m.u.
32: Total charge 0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 117
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (117 atoms, 16 residues)
32: Identified residue LYS50 as a starting terminus.
32: Identified residue PRO65 as a ending terminus.
32: Start terminus LYS-50: NH3+
32: End terminus PRO-65: PRO-COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 228 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
32: The Oplsaa force field and the tip4p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/15 (502 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/16
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 25 donors and 23 acceptors were found.
32: There are 41 hydrogen bonds
32: Will use HISE for residue 8
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS3 HIS8
32: SG9 NE251
32: HIS8 NE251 1.055
32: MET12 SD83 0.763 0.990
32: Making bonds...
32: Number of bonds was 254, now 254
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 653 pairs
32: Before cleaning: 663 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 663 dihedrals, 51 impropers, 457 angles
32: 650 pairs, 254 bonds and 0 virtual sites
32: Total mass 1846.112 a.m.u.
32: Total charge 0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 128
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (128 atoms, 16 residues)
32: Identified residue ALA2 as a starting terminus.
32: Identified residue SER17 as a ending terminus.
32: Start terminus ALA-2: NH3+
32: End terminus SER-17: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 252 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
32: The Oplsaa force field and the tip5p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/16 (498 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/17
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 30 donors and 22 acceptors were found.
32: There are 36 hydrogen bonds
32: Will use HISE for residue 29
32: Will use HISE for residue 32
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS27 HIS29
32: SG90 NE2111
32: HIS29 NE2111 0.987
32: HIS32 NE2135 1.590 1.155
32: Making bonds...
32: Number of bonds was 290, now 290
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 748 pairs
32: Before cleaning: 778 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 778 dihedrals, 72 impropers, 516 angles
32: 736 pairs, 290 bonds and 0 virtual sites
32: Total mass 2088.357 a.m.u.
32: Total charge 1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 149
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (149 atoms, 16 residues)
32: Identified residue THR18 as a starting terminus.
32: Identified residue PHE33 as a ending terminus.
32: Start terminus THR-18: NH3+
32: End terminus PHE-33: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 281 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
32: The Oplsaa force field and the tip5p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/17 (557 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/18
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 22 acceptors were found.
32: There are 26 hydrogen bonds
32: Will use HISE for residue 45
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS45
32: NE295
32: MET46 SD102 1.078
32: Making bonds...
32: Number of bonds was 261, now 261
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 676 pairs
32: Before cleaning: 696 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 696 dihedrals, 56 impropers, 472 angles
32: 667 pairs, 261 bonds and 0 virtual sites
32: Total mass 1861.128 a.m.u.
32: Total charge -1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 132
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (132 atoms, 16 residues)
32: Identified residue ALA34 as a starting terminus.
32: Identified residue ALA49 as a ending terminus.
32: Start terminus ALA-34: NH3+
32: End terminus ALA-49: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 255 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
32: The Oplsaa force field and the tip5p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/18 (506 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/19
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 21 acceptors were found.
32: There are 30 hydrogen bonds
32: Will use HISE for residue 60
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS60
32: NE285
32: CYS62 SG98 0.803
32: Making bonds...
32: Number of bonds was 232, now 232
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 603 pairs
32: Before cleaning: 618 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 618 dihedrals, 48 impropers, 419 angles
32: 597 pairs, 232 bonds and 0 virtual sites
32: Total mass 1662.883 a.m.u.
32: Total charge 0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 117
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (117 atoms, 16 residues)
32: Identified residue LYS50 as a starting terminus.
32: Identified residue PRO65 as a ending terminus.
32: Start terminus LYS-50: NH3+
32: End terminus PRO-65: PRO-COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 228 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
32: The Oplsaa force field and the tip5p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/19 (469 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/20
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 25 donors and 23 acceptors were found.
32: There are 41 hydrogen bonds
32: Will use HISE for residue 8
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS3 HIS8
32: SG9 NE251
32: HIS8 NE251 1.055
32: MET12 SD83 0.763 0.990
32: Making bonds...
32: Number of bonds was 254, now 254
32: Marked 124 virtual sites
32: Added 16 dummy masses
32: Added 26 new constraints
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 653 pairs
32: Before cleaning: 663 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 663 dihedrals, 51 impropers, 457 angles
32: 650 pairs, 254 bonds and 130 virtual sites
32: Total mass 1846.112 a.m.u.
32: Total charge 0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 128
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (128 atoms, 16 residues)
32: Identified residue ALA2 as a starting terminus.
32: Identified residue SER17 as a ending terminus.
32: Start terminus ALA-2: NH3+
32: End terminus SER-17: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 252 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
32: The Oplsaa force field and the tip5p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/20 (535 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/21
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 30 donors and 22 acceptors were found.
32: There are 36 hydrogen bonds
32: Will use HISE for residue 29
32: Will use HISE for residue 32
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS27 HIS29
32: SG90 NE2111
32: HIS29 NE2111 0.987
32: HIS32 NE2135 1.590 1.155
32: Making bonds...
32: Number of bonds was 290, now 290
32: Marked 132 virtual sites
32: Added 10 dummy masses
32: Added 19 new constraints
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 748 pairs
32: Before cleaning: 778 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 778 dihedrals, 72 impropers, 516 angles
32: 736 pairs, 290 bonds and 133 virtual sites
32: Total mass 2088.357 a.m.u.
32: Total charge 1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 149
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (149 atoms, 16 residues)
32: Identified residue THR18 as a starting terminus.
32: Identified residue PHE33 as a ending terminus.
32: Start terminus THR-18: NH3+
32: End terminus PHE-33: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 281 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
32: The Oplsaa force field and the tip5p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/21 (586 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/22
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 22 acceptors were found.
32: There are 26 hydrogen bonds
32: Will use HISE for residue 45
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS45
32: NE295
32: MET46 SD102 1.078
32: Making bonds...
32: Number of bonds was 261, now 261
32: Marked 123 virtual sites
32: Added 22 dummy masses
32: Added 35 new constraints
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 676 pairs
32: Before cleaning: 696 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 696 dihedrals, 56 impropers, 472 angles
32: 667 pairs, 261 bonds and 132 virtual sites
32: Total mass 1861.128 a.m.u.
32: Total charge -1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 132
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (132 atoms, 16 residues)
32: Identified residue ALA34 as a starting terminus.
32: Identified residue ALA49 as a ending terminus.
32: Start terminus ALA-34: NH3+
32: End terminus ALA-49: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 255 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
32: The Oplsaa force field and the tip5p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/22 (555 ms)
32: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/23
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 21 acceptors were found.
32: There are 30 hydrogen bonds
32: Will use HISE for residue 60
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS60
32: NE285
32: CYS62 SG98 0.803
32: Making bonds...
32: Number of bonds was 232, now 232
32: Marked 111 virtual sites
32: Added 18 dummy masses
32: Added 31 new constraints
32: Generating angles, dihedrals and pairs...
32: Before cleaning: 603 pairs
32: Before cleaning: 618 dihedrals
32: Keeping all generated dihedrals
32: Making cmap torsions...
32: There are 618 dihedrals, 48 impropers, 419 angles
32: 597 pairs, 232 bonds and 116 virtual sites
32: Total mass 1662.883 a.m.u.
32: Total charge 0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Oplsaa force field in directory oplsaa.ff
32:
32: going to rename oplsaa.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 117
32:
32: Reading residue database... (Oplsaa)
32: Processing chain 1 (117 atoms, 16 residues)
32: Identified residue LYS50 as a starting terminus.
32: Identified residue PRO65 as a ending terminus.
32: Start terminus LYS-50: NH3+
32: End terminus PRO-65: PRO-COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 228 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
32: The Oplsaa force field and the tip5p water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/23 (498 ms)
32: [----------] 24 tests from ForOplsaa/Pdb2gmxTest (12680 ms total)
32:
32: [----------] Global test environment tear-down
32: [==========] 24 tests from 1 test case ran. (12680 ms total)
32: [ PASSED ] 24 tests.
32/52 Test #32: Pdb2gmx1Test ........................ Passed 12.78 sec
test 33
Start 33: Pdb2gmx2Test
33: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/pdb2gmx2-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/Pdb2gmx2Test.xml"
33: Test timeout computed to be: 30
33: [==========] Running 32 tests from 2 test cases.
33: [----------] Global test environment set-up.
33: [----------] 16 tests from ForGromos43a1/Pdb2gmxTest
33: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/0
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 25 donors and 23 acceptors were found.
33: There are 41 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33: Making bonds...
33: Number of bonds was 172, now 167
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 267 pairs
33: Before cleaning: 305 dihedrals
33: Making cmap torsions...
33: There are 90 dihedrals, 77 impropers, 241 angles
33: 267 pairs, 167 bonds and 0 virtual sites
33: Total mass 1846.116 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos43a1 force field in directory gromos43a1.ff
33:
33: going to rename gromos43a1.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 128
33:
33: Reading residue database... (Gromos43a1)
33: Processing chain 1 (128 atoms, 16 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 165 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
33: The Gromos43a1 force field and the spc water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/0 (315 ms)
33: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/1
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 30 donors and 22 acceptors were found.
33: There are 36 hydrogen bonds
33: Will use HISE for residue 29
33: Will use HISE for residue 32
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS27 HIS29
33: SG90 NE2111
33: HIS29 NE2111 0.987
33: HIS32 NE2135 1.590 1.155
33: Making bonds...
33: Number of bonds was 216, now 211
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 273 pairs
33: Before cleaning: 429 dihedrals
33: Making cmap torsions...
33: There are 93 dihedrals, 134 impropers, 316 angles
33: 273 pairs, 211 bonds and 0 virtual sites
33: Total mass 2088.361 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos43a1 force field in directory gromos43a1.ff
33:
33: going to rename gromos43a1.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
33: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 149
33:
33: Reading residue database... (Gromos43a1)
33: Processing chain 1 (149 atoms, 16 residues)
33: Identified residue THR18 as a starting terminus.
33: Identified residue PHE33 as a ending terminus.
33: Start terminus THR-18: NH3+
33: End terminus PHE-33: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 202 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
33: The Gromos43a1 force field and the spc water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/1 (356 ms)
33: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/2
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 22 acceptors were found.
33: There are 26 hydrogen bonds
33: Will use HISE for residue 45
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS45
33: NE295
33: MET46 SD102 1.078
33: Making bonds...
33: Number of bonds was 179, now 174
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 242 pairs
33: Before cleaning: 349 dihedrals
33: Making cmap torsions...
33: There are 81 dihedrals, 102 impropers, 260 angles
33: 242 pairs, 174 bonds and 0 virtual sites
33: Total mass 1861.132 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos43a1 force field in directory gromos43a1.ff
33:
33: going to rename gromos43a1.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
33: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 132
33:
33: Reading residue database... (Gromos43a1)
33: Processing chain 1 (132 atoms, 16 residues)
33: Identified residue ALA34 as a starting terminus.
33: Identified residue ALA49 as a ending terminus.
33: Start terminus ALA-34: NH3+
33: End terminus ALA-49: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 168 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
33: The Gromos43a1 force field and the spc water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/2 (308 ms)
33: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/3
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 21 acceptors were found.
33: There are 30 hydrogen bonds
33: Will use HISE for residue 60
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS60
33: NE285
33: CYS62 SG98 0.803
33: Making bonds...
33: Number of bonds was 159, now 154
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 232 pairs
33: Before cleaning: 299 dihedrals
33: Making cmap torsions...
33: There are 78 dihedrals, 80 impropers, 227 angles
33: 232 pairs, 154 bonds and 0 virtual sites
33: Total mass 1662.887 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos43a1 force field in directory gromos43a1.ff
33:
33: going to rename gromos43a1.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
33: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 117
33:
33: Reading residue database... (Gromos43a1)
33: Processing chain 1 (117 atoms, 16 residues)
33: Identified residue LYS50 as a starting terminus.
33: Identified residue PRO65 as a ending terminus.
33: Start terminus LYS-50: NH3+
33: End terminus PRO-65: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 150 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
33: The Gromos43a1 force field and the spc water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/3 (288 ms)
33: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/4
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 25 donors and 23 acceptors were found.
33: There are 41 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33: Making bonds...
33: Number of bonds was 172, now 167
33: Marked 37 virtual sites
33: Added 4 dummy masses
33: Added 8 new constraints
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 267 pairs
33: Before cleaning: 305 dihedrals
33: Making cmap torsions...
33: There are 90 dihedrals, 77 impropers, 241 angles
33: 267 pairs, 167 bonds and 37 virtual sites
33: Total mass 1846.116 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos43a1 force field in directory gromos43a1.ff
33:
33: going to rename gromos43a1.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 128
33:
33: Reading residue database... (Gromos43a1)
33: Processing chain 1 (128 atoms, 16 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 165 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
33: The Gromos43a1 force field and the spc water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/4 (313 ms)
33: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/5
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 30 donors and 22 acceptors were found.
33: There are 36 hydrogen bonds
33: Will use HISE for residue 29
33: Will use HISE for residue 32
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS27 HIS29
33: SG90 NE2111
33: HIS29 NE2111 0.987
33: HIS32 NE2135 1.590 1.155
33: Making bonds...
33: Number of bonds was 216, now 211
33: Marked 53 virtual sites
33: Added 4 dummy masses
33: Added 10 new constraints
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 273 pairs
33: Before cleaning: 429 dihedrals
33: Making cmap torsions...
33: There are 93 dihedrals, 134 impropers, 316 angles
33: 273 pairs, 211 bonds and 51 virtual sites
33: Total mass 2088.361 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos43a1 force field in directory gromos43a1.ff
33:
33: going to rename gromos43a1.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
33: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 149
33:
33: Reading residue database... (Gromos43a1)
33: Processing chain 1 (149 atoms, 16 residues)
33: Identified residue THR18 as a starting terminus.
33: Identified residue PHE33 as a ending terminus.
33: Start terminus THR-18: NH3+
33: End terminus PHE-33: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 202 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
33: The Gromos43a1 force field and the spc water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/5 (362 ms)
33: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/6
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 22 acceptors were found.
33: There are 26 hydrogen bonds
33: Will use HISE for residue 45
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS45
33: NE295
33: MET46 SD102 1.078
33: Making bonds...
33: Number of bonds was 179, now 174
33: Marked 36 virtual sites
33: Added 4 dummy masses
33: Added 8 new constraints
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 242 pairs
33: Before cleaning: 349 dihedrals
33: Making cmap torsions...
33: There are 81 dihedrals, 102 impropers, 260 angles
33: 242 pairs, 174 bonds and 36 virtual sites
33: Total mass 1861.132 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos43a1 force field in directory gromos43a1.ff
33:
33: going to rename gromos43a1.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
33: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 132
33:
33: Reading residue database... (Gromos43a1)
33: Processing chain 1 (132 atoms, 16 residues)
33: Identified residue ALA34 as a starting terminus.
33: Identified residue ALA49 as a ending terminus.
33: Start terminus ALA-34: NH3+
33: End terminus ALA-49: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 168 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
33: The Gromos43a1 force field and the spc water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/6 (320 ms)
33: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/7
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 21 acceptors were found.
33: There are 30 hydrogen bonds
33: Will use HISE for residue 60
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS60
33: NE285
33: CYS62 SG98 0.803
33: Making bonds...
33: Number of bonds was 159, now 154
33: Marked 33 virtual sites
33: Added 4 dummy masses
33: Added 10 new constraints
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 232 pairs
33: Before cleaning: 299 dihedrals
33: Making cmap torsions...
33: There are 78 dihedrals, 80 impropers, 227 angles
33: 232 pairs, 154 bonds and 31 virtual sites
33: Total mass 1662.887 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos43a1 force field in directory gromos43a1.ff
33:
33: going to rename gromos43a1.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
33: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 117
33:
33: Reading residue database... (Gromos43a1)
33: Processing chain 1 (117 atoms, 16 residues)
33: Identified residue LYS50 as a starting terminus.
33: Identified residue PRO65 as a ending terminus.
33: Start terminus LYS-50: NH3+
33: End terminus PRO-65: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 150 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
33: The Gromos43a1 force field and the spc water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/7 (298 ms)
33: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/8
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 25 donors and 23 acceptors were found.
33: There are 41 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33: Making bonds...
33: Number of bonds was 172, now 167
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 267 pairs
33: Before cleaning: 305 dihedrals
33: Making cmap torsions...
33: There are 90 dihedrals, 77 impropers, 241 angles
33: 267 pairs, 167 bonds and 0 virtual sites
33: Total mass 1846.116 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos43a1 force field in directory gromos43a1.ff
33:
33: going to rename gromos43a1.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 128
33:
33: Reading residue database... (Gromos43a1)
33: Processing chain 1 (128 atoms, 16 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 165 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
33: The Gromos43a1 force field and the spce water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/8 (301 ms)
33: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/9
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 30 donors and 22 acceptors were found.
33: There are 36 hydrogen bonds
33: Will use HISE for residue 29
33: Will use HISE for residue 32
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS27 HIS29
33: SG90 NE2111
33: HIS29 NE2111 0.987
33: HIS32 NE2135 1.590 1.155
33: Making bonds...
33: Number of bonds was 216, now 211
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 273 pairs
33: Before cleaning: 429 dihedrals
33: Making cmap torsions...
33: There are 93 dihedrals, 134 impropers, 316 angles
33: 273 pairs, 211 bonds and 0 virtual sites
33: Total mass 2088.361 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos43a1 force field in directory gromos43a1.ff
33:
33: going to rename gromos43a1.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
33: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 149
33:
33: Reading residue database... (Gromos43a1)
33: Processing chain 1 (149 atoms, 16 residues)
33: Identified residue THR18 as a starting terminus.
33: Identified residue PHE33 as a ending terminus.
33: Start terminus THR-18: NH3+
33: End terminus PHE-33: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 202 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
33: The Gromos43a1 force field and the spce water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/9 (351 ms)
33: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/10
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 22 acceptors were found.
33: There are 26 hydrogen bonds
33: Will use HISE for residue 45
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS45
33: NE295
33: MET46 SD102 1.078
33: Making bonds...
33: Number of bonds was 179, now 174
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 242 pairs
33: Before cleaning: 349 dihedrals
33: Making cmap torsions...
33: There are 81 dihedrals, 102 impropers, 260 angles
33: 242 pairs, 174 bonds and 0 virtual sites
33: Total mass 1861.132 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos43a1 force field in directory gromos43a1.ff
33:
33: going to rename gromos43a1.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
33: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 132
33:
33: Reading residue database... (Gromos43a1)
33: Processing chain 1 (132 atoms, 16 residues)
33: Identified residue ALA34 as a starting terminus.
33: Identified residue ALA49 as a ending terminus.
33: Start terminus ALA-34: NH3+
33: End terminus ALA-49: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 168 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
33: The Gromos43a1 force field and the spce water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/10 (309 ms)
33: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/11
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 21 acceptors were found.
33: There are 30 hydrogen bonds
33: Will use HISE for residue 60
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS60
33: NE285
33: CYS62 SG98 0.803
33: Making bonds...
33: Number of bonds was 159, now 154
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 232 pairs
33: Before cleaning: 299 dihedrals
33: Making cmap torsions...
33: There are 78 dihedrals, 80 impropers, 227 angles
33: 232 pairs, 154 bonds and 0 virtual sites
33: Total mass 1662.887 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos43a1 force field in directory gromos43a1.ff
33:
33: going to rename gromos43a1.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
33: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 117
33:
33: Reading residue database... (Gromos43a1)
33: Processing chain 1 (117 atoms, 16 residues)
33: Identified residue LYS50 as a starting terminus.
33: Identified residue PRO65 as a ending terminus.
33: Start terminus LYS-50: NH3+
33: End terminus PRO-65: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 150 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
33: The Gromos43a1 force field and the spce water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/11 (286 ms)
33: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/12
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 25 donors and 23 acceptors were found.
33: There are 41 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33: Making bonds...
33: Number of bonds was 172, now 167
33: Marked 37 virtual sites
33: Added 4 dummy masses
33: Added 8 new constraints
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 267 pairs
33: Before cleaning: 305 dihedrals
33: Making cmap torsions...
33: There are 90 dihedrals, 77 impropers, 241 angles
33: 267 pairs, 167 bonds and 37 virtual sites
33: Total mass 1846.116 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos43a1 force field in directory gromos43a1.ff
33:
33: going to rename gromos43a1.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 128
33:
33: Reading residue database... (Gromos43a1)
33: Processing chain 1 (128 atoms, 16 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 165 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
33: The Gromos43a1 force field and the spce water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/12 (314 ms)
33: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/13
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 30 donors and 22 acceptors were found.
33: There are 36 hydrogen bonds
33: Will use HISE for residue 29
33: Will use HISE for residue 32
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS27 HIS29
33: SG90 NE2111
33: HIS29 NE2111 0.987
33: HIS32 NE2135 1.590 1.155
33: Making bonds...
33: Number of bonds was 216, now 211
33: Marked 53 virtual sites
33: Added 4 dummy masses
33: Added 10 new constraints
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 273 pairs
33: Before cleaning: 429 dihedrals
33: Making cmap torsions...
33: There are 93 dihedrals, 134 impropers, 316 angles
33: 273 pairs, 211 bonds and 51 virtual sites
33: Total mass 2088.361 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos43a1 force field in directory gromos43a1.ff
33:
33: going to rename gromos43a1.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
33: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 149
33:
33: Reading residue database... (Gromos43a1)
33: Processing chain 1 (149 atoms, 16 residues)
33: Identified residue THR18 as a starting terminus.
33: Identified residue PHE33 as a ending terminus.
33: Start terminus THR-18: NH3+
33: End terminus PHE-33: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 202 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
33: The Gromos43a1 force field and the spce water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/13 (365 ms)
33: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/14
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 22 acceptors were found.
33: There are 26 hydrogen bonds
33: Will use HISE for residue 45
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS45
33: NE295
33: MET46 SD102 1.078
33: Making bonds...
33: Number of bonds was 179, now 174
33: Marked 36 virtual sites
33: Added 4 dummy masses
33: Added 8 new constraints
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 242 pairs
33: Before cleaning: 349 dihedrals
33: Making cmap torsions...
33: There are 81 dihedrals, 102 impropers, 260 angles
33: 242 pairs, 174 bonds and 36 virtual sites
33: Total mass 1861.132 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos43a1 force field in directory gromos43a1.ff
33:
33: going to rename gromos43a1.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
33: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 132
33:
33: Reading residue database... (Gromos43a1)
33: Processing chain 1 (132 atoms, 16 residues)
33: Identified residue ALA34 as a starting terminus.
33: Identified residue ALA49 as a ending terminus.
33: Start terminus ALA-34: NH3+
33: End terminus ALA-49: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 168 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
33: The Gromos43a1 force field and the spce water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/14 (319 ms)
33: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/15
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 21 acceptors were found.
33: There are 30 hydrogen bonds
33: Will use HISE for residue 60
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS60
33: NE285
33: CYS62 SG98 0.803
33: Making bonds...
33: Number of bonds was 159, now 154
33: Marked 33 virtual sites
33: Added 4 dummy masses
33: Added 10 new constraints
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 232 pairs
33: Before cleaning: 299 dihedrals
33: Making cmap torsions...
33: There are 78 dihedrals, 80 impropers, 227 angles
33: 232 pairs, 154 bonds and 31 virtual sites
33: Total mass 1662.887 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos43a1 force field in directory gromos43a1.ff
33:
33: going to rename gromos43a1.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
33: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 117
33:
33: Reading residue database... (Gromos43a1)
33: Processing chain 1 (117 atoms, 16 residues)
33: Identified residue LYS50 as a starting terminus.
33: Identified residue PRO65 as a ending terminus.
33: Start terminus LYS-50: NH3+
33: End terminus PRO-65: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 150 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
33: The Gromos43a1 force field and the spce water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/15 (301 ms)
33: [----------] 16 tests from ForGromos43a1/Pdb2gmxTest (5107 ms total)
33:
33: [----------] 16 tests from ForGromos53a6/Pdb2gmxTest
33: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/0
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
33: Using default: not generating all possible dihedrals
33: Using default: excluding 3 bonded neighbors
33: Using default: generating 1,4 H--H interactions
33: Using default: removing proper dihedrals found on the same bond as a proper dihedral
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 25 donors and 23 acceptors were found.
33: There are 41 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33: Making bonds...
33: Number of bonds was 174, now 169
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 267 pairs
33: Before cleaning: 312 dihedrals
33: Making cmap torsions...
33: There are 90 dihedrals, 79 impropers, 245 angles
33: 267 pairs, 169 bonds and 0 virtual sites
33: Total mass 1846.116 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos53a6 force field in directory gromos53a6.ff
33:
33: going to rename gromos53a6.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 128
33:
33: Reading residue database... (Gromos53a6)
33: Processing chain 1 (128 atoms, 16 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 167 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
33: The Gromos53a6 force field and the spc water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/0 (337 ms)
33: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/1
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
33: Using default: not generating all possible dihedrals
33: Using default: excluding 3 bonded neighbors
33: Using default: generating 1,4 H--H interactions
33: Using default: removing proper dihedrals found on the same bond as a proper dihedral
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 30 donors and 22 acceptors were found.
33: There are 36 hydrogen bonds
33: Will use HISE for residue 29
33: Will use HISE for residue 32
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS27 HIS29
33: SG90 NE2111
33: HIS29 NE2111 0.987
33: HIS32 NE2135 1.590 1.155
33: Making bonds...
33: Number of bonds was 220, now 215
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 273 pairs
33: Before cleaning: 443 dihedrals
33: Making cmap torsions...
33: There are 93 dihedrals, 138 impropers, 324 angles
33: 273 pairs, 215 bonds and 0 virtual sites
33: Total mass 2088.361 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos53a6 force field in directory gromos53a6.ff
33:
33: going to rename gromos53a6.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
33: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 149
33:
33: Reading residue database... (Gromos53a6)
33: Processing chain 1 (149 atoms, 16 residues)
33: Identified residue THR18 as a starting terminus.
33: Identified residue PHE33 as a ending terminus.
33: Start terminus THR-18: NH3+
33: End terminus PHE-33: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 206 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
33: The Gromos53a6 force field and the spc water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/1 (382 ms)
33: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/2
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
33: Using default: not generating all possible dihedrals
33: Using default: excluding 3 bonded neighbors
33: Using default: generating 1,4 H--H interactions
33: Using default: removing proper dihedrals found on the same bond as a proper dihedral
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 22 acceptors were found.
33: There are 26 hydrogen bonds
33: Will use HISE for residue 45
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS45
33: NE295
33: MET46 SD102 1.078
33: Making bonds...
33: Number of bonds was 181, now 176
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 242 pairs
33: Before cleaning: 356 dihedrals
33: Making cmap torsions...
33: There are 81 dihedrals, 104 impropers, 264 angles
33: 242 pairs, 176 bonds and 0 virtual sites
33: Total mass 1861.132 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos53a6 force field in directory gromos53a6.ff
33:
33: going to rename gromos53a6.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
33: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 132
33:
33: Reading residue database... (Gromos53a6)
33: Processing chain 1 (132 atoms, 16 residues)
33: Identified residue ALA34 as a starting terminus.
33: Identified residue ALA49 as a ending terminus.
33: Start terminus ALA-34: NH3+
33: End terminus ALA-49: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 170 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
33: The Gromos53a6 force field and the spc water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/2 (337 ms)
33: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/3
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
33: Using default: not generating all possible dihedrals
33: Using default: excluding 3 bonded neighbors
33: Using default: generating 1,4 H--H interactions
33: Using default: removing proper dihedrals found on the same bond as a proper dihedral
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 21 acceptors were found.
33: There are 30 hydrogen bonds
33: Will use HISE for residue 60
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS60
33: NE285
33: CYS62 SG98 0.803
33: Making bonds...
33: Number of bonds was 161, now 156
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 232 pairs
33: Before cleaning: 306 dihedrals
33: Making cmap torsions...
33: There are 78 dihedrals, 82 impropers, 231 angles
33: 232 pairs, 156 bonds and 0 virtual sites
33: Total mass 1662.887 a.m.u.
33: Total charge -0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos53a6 force field in directory gromos53a6.ff
33:
33: going to rename gromos53a6.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
33: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 117
33:
33: Reading residue database... (Gromos53a6)
33: Processing chain 1 (117 atoms, 16 residues)
33: Identified residue LYS50 as a starting terminus.
33: Identified residue PRO65 as a ending terminus.
33: Start terminus LYS-50: NH3+
33: End terminus PRO-65: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 152 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
33: The Gromos53a6 force field and the spc water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/3 (316 ms)
33: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/4
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
33: Using default: not generating all possible dihedrals
33: Using default: excluding 3 bonded neighbors
33: Using default: generating 1,4 H--H interactions
33: Using default: removing proper dihedrals found on the same bond as a proper dihedral
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 25 donors and 23 acceptors were found.
33: There are 41 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33: Making bonds...
33: Number of bonds was 174, now 169
33: Marked 39 virtual sites
33: Added 4 dummy masses
33: Added 8 new constraints
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 267 pairs
33: Before cleaning: 312 dihedrals
33: Making cmap torsions...
33: There are 90 dihedrals, 79 impropers, 245 angles
33: 267 pairs, 169 bonds and 39 virtual sites
33: Total mass 1846.116 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos53a6 force field in directory gromos53a6.ff
33:
33: going to rename gromos53a6.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 128
33:
33: Reading residue database... (Gromos53a6)
33: Processing chain 1 (128 atoms, 16 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 167 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
33: The Gromos53a6 force field and the spc water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/4 (343 ms)
33: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/5
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
33: Using default: not generating all possible dihedrals
33: Using default: excluding 3 bonded neighbors
33: Using default: generating 1,4 H--H interactions
33: Using default: removing proper dihedrals found on the same bond as a proper dihedral
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 30 donors and 22 acceptors were found.
33: There are 36 hydrogen bonds
33: Will use HISE for residue 29
33: Will use HISE for residue 32
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS27 HIS29
33: SG90 NE2111
33: HIS29 NE2111 0.987
33: HIS32 NE2135 1.590 1.155
33: Making bonds...
33: Number of bonds was 220, now 215
33: Marked 57 virtual sites
33: Added 4 dummy masses
33: Added 10 new constraints
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 273 pairs
33: Before cleaning: 443 dihedrals
33: Making cmap torsions...
33: There are 93 dihedrals, 138 impropers, 324 angles
33: 273 pairs, 215 bonds and 55 virtual sites
33: Total mass 2088.361 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos53a6 force field in directory gromos53a6.ff
33:
33: going to rename gromos53a6.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
33: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 149
33:
33: Reading residue database... (Gromos53a6)
33: Processing chain 1 (149 atoms, 16 residues)
33: Identified residue THR18 as a starting terminus.
33: Identified residue PHE33 as a ending terminus.
33: Start terminus THR-18: NH3+
33: End terminus PHE-33: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 206 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
33: The Gromos53a6 force field and the spc water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/5 (395 ms)
33: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/6
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
33: Using default: not generating all possible dihedrals
33: Using default: excluding 3 bonded neighbors
33: Using default: generating 1,4 H--H interactions
33: Using default: removing proper dihedrals found on the same bond as a proper dihedral
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 22 acceptors were found.
33: There are 26 hydrogen bonds
33: Will use HISE for residue 45
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS45
33: NE295
33: MET46 SD102 1.078
33: Making bonds...
33: Number of bonds was 181, now 176
33: Marked 38 virtual sites
33: Added 4 dummy masses
33: Added 8 new constraints
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 242 pairs
33: Before cleaning: 356 dihedrals
33: Making cmap torsions...
33: There are 81 dihedrals, 104 impropers, 264 angles
33: 242 pairs, 176 bonds and 38 virtual sites
33: Total mass 1861.132 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos53a6 force field in directory gromos53a6.ff
33:
33: going to rename gromos53a6.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
33: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 132
33:
33: Reading residue database... (Gromos53a6)
33: Processing chain 1 (132 atoms, 16 residues)
33: Identified residue ALA34 as a starting terminus.
33: Identified residue ALA49 as a ending terminus.
33: Start terminus ALA-34: NH3+
33: End terminus ALA-49: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 170 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
33: The Gromos53a6 force field and the spc water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/6 (349 ms)
33: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/7
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
33: Using default: not generating all possible dihedrals
33: Using default: excluding 3 bonded neighbors
33: Using default: generating 1,4 H--H interactions
33: Using default: removing proper dihedrals found on the same bond as a proper dihedral
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 21 acceptors were found.
33: There are 30 hydrogen bonds
33: Will use HISE for residue 60
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS60
33: NE285
33: CYS62 SG98 0.803
33: Making bonds...
33: Number of bonds was 161, now 156
33: Marked 35 virtual sites
33: Added 4 dummy masses
33: Added 10 new constraints
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 232 pairs
33: Before cleaning: 306 dihedrals
33: Making cmap torsions...
33: There are 78 dihedrals, 82 impropers, 231 angles
33: 232 pairs, 156 bonds and 33 virtual sites
33: Total mass 1662.887 a.m.u.
33: Total charge -0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos53a6 force field in directory gromos53a6.ff
33:
33: going to rename gromos53a6.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
33: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 117
33:
33: Reading residue database... (Gromos53a6)
33: Processing chain 1 (117 atoms, 16 residues)
33: Identified residue LYS50 as a starting terminus.
33: Identified residue PRO65 as a ending terminus.
33: Start terminus LYS-50: NH3+
33: End terminus PRO-65: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 152 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
33: The Gromos53a6 force field and the spc water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/7 (327 ms)
33: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/8
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
33: Using default: not generating all possible dihedrals
33: Using default: excluding 3 bonded neighbors
33: Using default: generating 1,4 H--H interactions
33: Using default: removing proper dihedrals found on the same bond as a proper dihedral
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 25 donors and 23 acceptors were found.
33: There are 41 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33: Making bonds...
33: Number of bonds was 174, now 169
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 267 pairs
33: Before cleaning: 312 dihedrals
33: Making cmap torsions...
33: There are 90 dihedrals, 79 impropers, 245 angles
33: 267 pairs, 169 bonds and 0 virtual sites
33: Total mass 1846.116 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos53a6 force field in directory gromos53a6.ff
33:
33: going to rename gromos53a6.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 128
33:
33: Reading residue database... (Gromos53a6)
33: Processing chain 1 (128 atoms, 16 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 167 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
33: The Gromos53a6 force field and the spce water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/8 (335 ms)
33: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/9
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
33: Using default: not generating all possible dihedrals
33: Using default: excluding 3 bonded neighbors
33: Using default: generating 1,4 H--H interactions
33: Using default: removing proper dihedrals found on the same bond as a proper dihedral
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 30 donors and 22 acceptors were found.
33: There are 36 hydrogen bonds
33: Will use HISE for residue 29
33: Will use HISE for residue 32
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS27 HIS29
33: SG90 NE2111
33: HIS29 NE2111 0.987
33: HIS32 NE2135 1.590 1.155
33: Making bonds...
33: Number of bonds was 220, now 215
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 273 pairs
33: Before cleaning: 443 dihedrals
33: Making cmap torsions...
33: There are 93 dihedrals, 138 impropers, 324 angles
33: 273 pairs, 215 bonds and 0 virtual sites
33: Total mass 2088.361 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos53a6 force field in directory gromos53a6.ff
33:
33: going to rename gromos53a6.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
33: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 149
33:
33: Reading residue database... (Gromos53a6)
33: Processing chain 1 (149 atoms, 16 residues)
33: Identified residue THR18 as a starting terminus.
33: Identified residue PHE33 as a ending terminus.
33: Start terminus THR-18: NH3+
33: End terminus PHE-33: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 206 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
33: The Gromos53a6 force field and the spce water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/9 (383 ms)
33: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/10
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
33: Using default: not generating all possible dihedrals
33: Using default: excluding 3 bonded neighbors
33: Using default: generating 1,4 H--H interactions
33: Using default: removing proper dihedrals found on the same bond as a proper dihedral
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 22 acceptors were found.
33: There are 26 hydrogen bonds
33: Will use HISE for residue 45
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS45
33: NE295
33: MET46 SD102 1.078
33: Making bonds...
33: Number of bonds was 181, now 176
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 242 pairs
33: Before cleaning: 356 dihedrals
33: Making cmap torsions...
33: There are 81 dihedrals, 104 impropers, 264 angles
33: 242 pairs, 176 bonds and 0 virtual sites
33: Total mass 1861.132 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos53a6 force field in directory gromos53a6.ff
33:
33: going to rename gromos53a6.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
33: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 132
33:
33: Reading residue database... (Gromos53a6)
33: Processing chain 1 (132 atoms, 16 residues)
33: Identified residue ALA34 as a starting terminus.
33: Identified residue ALA49 as a ending terminus.
33: Start terminus ALA-34: NH3+
33: End terminus ALA-49: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 170 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
33: The Gromos53a6 force field and the spce water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/10 (338 ms)
33: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/11
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
33: Using default: not generating all possible dihedrals
33: Using default: excluding 3 bonded neighbors
33: Using default: generating 1,4 H--H interactions
33: Using default: removing proper dihedrals found on the same bond as a proper dihedral
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 21 acceptors were found.
33: There are 30 hydrogen bonds
33: Will use HISE for residue 60
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS60
33: NE285
33: CYS62 SG98 0.803
33: Making bonds...
33: Number of bonds was 161, now 156
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 232 pairs
33: Before cleaning: 306 dihedrals
33: Making cmap torsions...
33: There are 78 dihedrals, 82 impropers, 231 angles
33: 232 pairs, 156 bonds and 0 virtual sites
33: Total mass 1662.887 a.m.u.
33: Total charge -0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos53a6 force field in directory gromos53a6.ff
33:
33: going to rename gromos53a6.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
33: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 117
33:
33: Reading residue database... (Gromos53a6)
33: Processing chain 1 (117 atoms, 16 residues)
33: Identified residue LYS50 as a starting terminus.
33: Identified residue PRO65 as a ending terminus.
33: Start terminus LYS-50: NH3+
33: End terminus PRO-65: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 152 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
33: The Gromos53a6 force field and the spce water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/11 (317 ms)
33: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/12
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
33: Using default: not generating all possible dihedrals
33: Using default: excluding 3 bonded neighbors
33: Using default: generating 1,4 H--H interactions
33: Using default: removing proper dihedrals found on the same bond as a proper dihedral
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 25 donors and 23 acceptors were found.
33: There are 41 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33: Making bonds...
33: Number of bonds was 174, now 169
33: Marked 39 virtual sites
33: Added 4 dummy masses
33: Added 8 new constraints
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 267 pairs
33: Before cleaning: 312 dihedrals
33: Making cmap torsions...
33: There are 90 dihedrals, 79 impropers, 245 angles
33: 267 pairs, 169 bonds and 39 virtual sites
33: Total mass 1846.116 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos53a6 force field in directory gromos53a6.ff
33:
33: going to rename gromos53a6.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 128
33:
33: Reading residue database... (Gromos53a6)
33: Processing chain 1 (128 atoms, 16 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 167 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
33: The Gromos53a6 force field and the spce water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/12 (343 ms)
33: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/13
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
33: Using default: not generating all possible dihedrals
33: Using default: excluding 3 bonded neighbors
33: Using default: generating 1,4 H--H interactions
33: Using default: removing proper dihedrals found on the same bond as a proper dihedral
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 30 donors and 22 acceptors were found.
33: There are 36 hydrogen bonds
33: Will use HISE for residue 29
33: Will use HISE for residue 32
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS27 HIS29
33: SG90 NE2111
33: HIS29 NE2111 0.987
33: HIS32 NE2135 1.590 1.155
33: Making bonds...
33: Number of bonds was 220, now 215
33: Marked 57 virtual sites
33: Added 4 dummy masses
33: Added 10 new constraints
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 273 pairs
33: Before cleaning: 443 dihedrals
33: Making cmap torsions...
33: There are 93 dihedrals, 138 impropers, 324 angles
33: 273 pairs, 215 bonds and 55 virtual sites
33: Total mass 2088.361 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos53a6 force field in directory gromos53a6.ff
33:
33: going to rename gromos53a6.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
33: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 149
33:
33: Reading residue database... (Gromos53a6)
33: Processing chain 1 (149 atoms, 16 residues)
33: Identified residue THR18 as a starting terminus.
33: Identified residue PHE33 as a ending terminus.
33: Start terminus THR-18: NH3+
33: End terminus PHE-33: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 206 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
33: The Gromos53a6 force field and the spce water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/13 (395 ms)
33: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/14
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
33: Using default: not generating all possible dihedrals
33: Using default: excluding 3 bonded neighbors
33: Using default: generating 1,4 H--H interactions
33: Using default: removing proper dihedrals found on the same bond as a proper dihedral
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 22 acceptors were found.
33: There are 26 hydrogen bonds
33: Will use HISE for residue 45
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS45
33: NE295
33: MET46 SD102 1.078
33: Making bonds...
33: Number of bonds was 181, now 176
33: Marked 38 virtual sites
33: Added 4 dummy masses
33: Added 8 new constraints
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 242 pairs
33: Before cleaning: 356 dihedrals
33: Making cmap torsions...
33: There are 81 dihedrals, 104 impropers, 264 angles
33: 242 pairs, 176 bonds and 38 virtual sites
33: Total mass 1861.132 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos53a6 force field in directory gromos53a6.ff
33:
33: going to rename gromos53a6.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
33: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 132
33:
33: Reading residue database... (Gromos53a6)
33: Processing chain 1 (132 atoms, 16 residues)
33: Identified residue ALA34 as a starting terminus.
33: Identified residue ALA49 as a ending terminus.
33: Start terminus ALA-34: NH3+
33: End terminus ALA-49: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 170 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
33: The Gromos53a6 force field and the spce water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/14 (349 ms)
33: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/15
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
33: Using default: not generating all possible dihedrals
33: Using default: excluding 3 bonded neighbors
33: Using default: generating 1,4 H--H interactions
33: Using default: removing proper dihedrals found on the same bond as a proper dihedral
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 21 acceptors were found.
33: There are 30 hydrogen bonds
33: Will use HISE for residue 60
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS60
33: NE285
33: CYS62 SG98 0.803
33: Making bonds...
33: Number of bonds was 161, now 156
33: Marked 35 virtual sites
33: Added 4 dummy masses
33: Added 10 new constraints
33: Generating angles, dihedrals and pairs...
33:
33: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom H used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33:
33: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
33: to an entry in the topology database, but the atom O used in
33: an interaction of type angle in that entry is not found in the
33: input file. Perhaps your atom and/or residue naming needs to be
33: fixed.
33:
33:
33: Before cleaning: 232 pairs
33: Before cleaning: 306 dihedrals
33: Making cmap torsions...
33: There are 78 dihedrals, 82 impropers, 231 angles
33: 232 pairs, 156 bonds and 33 virtual sites
33: Total mass 1662.887 a.m.u.
33: Total charge -0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Gromos53a6 force field in directory gromos53a6.ff
33:
33: going to rename gromos53a6.ff/aminoacids.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
33: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 117
33:
33: Reading residue database... (Gromos53a6)
33: Processing chain 1 (117 atoms, 16 residues)
33: Identified residue LYS50 as a starting terminus.
33: Identified residue PRO65 as a ending terminus.
33: Start terminus LYS-50: NH3+
33: End terminus PRO-65: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 152 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
33: The Gromos53a6 force field and the spce water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/15 (327 ms)
33: [----------] 16 tests from ForGromos53a6/Pdb2gmxTest (5573 ms total)
33:
33: [----------] Global test environment tear-down
33: [==========] 32 tests from 2 test cases ran. (10681 ms total)
33: [ PASSED ] 32 tests.
33/52 Test #33: Pdb2gmx2Test ........................ Passed 10.75 sec
test 34
Start 34: Pdb2gmx3Test
34: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/pdb2gmx3-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/Pdb2gmx3Test.xml"
34: Test timeout computed to be: 30
34: [==========] Running 28 tests from 4 test cases.
34: [----------] Global test environment set-up.
34: [----------] 8 tests from ForAmber99sb_ildn/Pdb2gmxTest
34: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/0
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 25 donors and 23 acceptors were found.
34: There are 41 hydrogen bonds
34: Will use HISE for residue 8
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: CYS3 HIS8
34: SG9 NE251
34: HIS8 NE251 1.055
34: MET12 SD83 0.763 0.990
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
34: Making bonds...
34: Number of bonds was 255, now 254
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 653 pairs
34: Before cleaning: 691 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 691 dihedrals, 51 impropers, 457 angles
34: 650 pairs, 254 bonds and 0 virtual sites
34: Total mass 1846.132 a.m.u.
34: Total charge 0.000 e
34: Writing topology
34:
34: Writing coordinate file...
34:
34: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
34:
34: going to rename amber99sb-ildn.ff/aminoacids.r2b
34: going to rename amber99sb-ildn.ff/dna.r2b
34: going to rename amber99sb-ildn.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
34: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records or chain id changing.
34: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
34:
34: chain #res #atoms
34: 1 ' ' 16 128
34:
34: Reading residue database... (Amber99sb-ildn)
34: Processing chain 1 (128 atoms, 16 residues)
34: Identified residue ALA2 as a starting terminus.
34: Identified residue SER17 as a ending terminus.
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 16 residues with 252 atoms
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
34: The Amber99sb-ildn force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/0 (431 ms)
34: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/1
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 30 donors and 22 acceptors were found.
34: There are 36 hydrogen bonds
34: Will use HISE for residue 29
34: Will use HISE for residue 32
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: CYS27 HIS29
34: SG90 NE2111
34: HIS29 NE2111 0.987
34: HIS32 NE2135 1.590 1.155
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
34: Making bonds...
34: Number of bonds was 291, now 290
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 748 pairs
34: Before cleaning: 788 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 788 dihedrals, 72 impropers, 516 angles
34: 736 pairs, 290 bonds and 0 virtual sites
34: Total mass 2088.366 a.m.u.
34: Total charge 1.000 e
34: Writing topology
34:
34: Writing coordinate file...
34:
34: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
34:
34: going to rename amber99sb-ildn.ff/aminoacids.r2b
34: going to rename amber99sb-ildn.ff/dna.r2b
34: going to rename amber99sb-ildn.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
34: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records or chain id changing.
34: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
34:
34: chain #res #atoms
34: 1 ' ' 16 149
34:
34: Reading residue database... (Amber99sb-ildn)
34: Processing chain 1 (149 atoms, 16 residues)
34: Identified residue THR18 as a starting terminus.
34: Identified residue PHE33 as a ending terminus.
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 16 residues with 281 atoms
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
34: The Amber99sb-ildn force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/1 (482 ms)
34: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/2
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 22 donors and 22 acceptors were found.
34: There are 26 hydrogen bonds
34: Will use HISE for residue 45
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: HIS45
34: NE295
34: MET46 SD102 1.078
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
34: Making bonds...
34: Number of bonds was 262, now 261
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 676 pairs
34: Before cleaning: 727 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 727 dihedrals, 56 impropers, 472 angles
34: 667 pairs, 261 bonds and 0 virtual sites
34: Total mass 1861.124 a.m.u.
34: Total charge -1.000 e
34: Writing topology
34:
34: Writing coordinate file...
34:
34: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
34:
34: going to rename amber99sb-ildn.ff/aminoacids.r2b
34: going to rename amber99sb-ildn.ff/dna.r2b
34: going to rename amber99sb-ildn.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
34: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records or chain id changing.
34: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
34:
34: chain #res #atoms
34: 1 ' ' 16 132
34:
34: Reading residue database... (Amber99sb-ildn)
34: Processing chain 1 (132 atoms, 16 residues)
34: Identified residue ALA34 as a starting terminus.
34: Identified residue ALA49 as a ending terminus.
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 16 residues with 255 atoms
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
34: The Amber99sb-ildn force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/2 (434 ms)
34: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/3
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 22 donors and 21 acceptors were found.
34: There are 30 hydrogen bonds
34: Will use HISE for residue 60
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: HIS60
34: NE285
34: CYS62 SG98 0.803
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
34: Making bonds...
34: Number of bonds was 233, now 232
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 603 pairs
34: Before cleaning: 634 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 634 dihedrals, 48 impropers, 419 angles
34: 597 pairs, 232 bonds and 0 virtual sites
34: Total mass 1662.888 a.m.u.
34: Total charge 0.000 e
34: Writing topology
34:
34: Writing coordinate file...
34:
34: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
34:
34: going to rename amber99sb-ildn.ff/aminoacids.r2b
34: going to rename amber99sb-ildn.ff/dna.r2b
34: going to rename amber99sb-ildn.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
34: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records or chain id changing.
34: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
34:
34: chain #res #atoms
34: 1 ' ' 16 117
34:
34: Reading residue database... (Amber99sb-ildn)
34: Processing chain 1 (117 atoms, 16 residues)
34: Identified residue LYS50 as a starting terminus.
34: Identified residue PRO65 as a ending terminus.
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 16 residues with 228 atoms
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
34: The Amber99sb-ildn force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/3 (393 ms)
34: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/4
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 25 donors and 23 acceptors were found.
34: There are 41 hydrogen bonds
34: Will use HISE for residue 8
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: CYS3 HIS8
34: SG9 NE251
34: HIS8 NE251 1.055
34: MET12 SD83 0.763 0.990
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
34: Making bonds...
34: Number of bonds was 255, now 254
34: Marked 124 virtual sites
34: Added 16 dummy masses
34: Added 26 new constraints
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 653 pairs
34: Before cleaning: 691 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 691 dihedrals, 51 impropers, 457 angles
34: 650 pairs, 254 bonds and 130 virtual sites
34: Total mass 1846.132 a.m.u.
34: Total charge 0.000 e
34: Writing topology
34:
34: Writing coordinate file...
34:
34: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
34:
34: going to rename amber99sb-ildn.ff/aminoacids.r2b
34: going to rename amber99sb-ildn.ff/dna.r2b
34: going to rename amber99sb-ildn.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
34: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records or chain id changing.
34: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
34:
34: chain #res #atoms
34: 1 ' ' 16 128
34:
34: Reading residue database... (Amber99sb-ildn)
34: Processing chain 1 (128 atoms, 16 residues)
34: Identified residue ALA2 as a starting terminus.
34: Identified residue SER17 as a ending terminus.
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 16 residues with 252 atoms
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
34: The Amber99sb-ildn force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/4 (461 ms)
34: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/5
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 30 donors and 22 acceptors were found.
34: There are 36 hydrogen bonds
34: Will use HISE for residue 29
34: Will use HISE for residue 32
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: CYS27 HIS29
34: SG90 NE2111
34: HIS29 NE2111 0.987
34: HIS32 NE2135 1.590 1.155
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
34: Making bonds...
34: Number of bonds was 291, now 290
34: Marked 132 virtual sites
34: Added 10 dummy masses
34: Added 19 new constraints
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 748 pairs
34: Before cleaning: 788 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 788 dihedrals, 72 impropers, 516 angles
34: 736 pairs, 290 bonds and 133 virtual sites
34: Total mass 2088.366 a.m.u.
34: Total charge 1.000 e
34: Writing topology
34:
34: Writing coordinate file...
34:
34: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
34:
34: going to rename amber99sb-ildn.ff/aminoacids.r2b
34: going to rename amber99sb-ildn.ff/dna.r2b
34: going to rename amber99sb-ildn.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
34: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records or chain id changing.
34: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
34:
34: chain #res #atoms
34: 1 ' ' 16 149
34:
34: Reading residue database... (Amber99sb-ildn)
34: Processing chain 1 (149 atoms, 16 residues)
34: Identified residue THR18 as a starting terminus.
34: Identified residue PHE33 as a ending terminus.
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 16 residues with 281 atoms
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
34: The Amber99sb-ildn force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/5 (512 ms)
34: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/6
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 22 donors and 22 acceptors were found.
34: There are 26 hydrogen bonds
34: Will use HISE for residue 45
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: HIS45
34: NE295
34: MET46 SD102 1.078
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
34: Making bonds...
34: Number of bonds was 262, now 261
34: Marked 123 virtual sites
34: Added 22 dummy masses
34: Added 35 new constraints
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 676 pairs
34: Before cleaning: 727 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 727 dihedrals, 56 impropers, 472 angles
34: 667 pairs, 261 bonds and 132 virtual sites
34: Total mass 1861.124 a.m.u.
34: Total charge -1.000 e
34: Writing topology
34:
34: Writing coordinate file...
34:
34: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
34:
34: going to rename amber99sb-ildn.ff/aminoacids.r2b
34: going to rename amber99sb-ildn.ff/dna.r2b
34: going to rename amber99sb-ildn.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
34: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records or chain id changing.
34: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
34:
34: chain #res #atoms
34: 1 ' ' 16 132
34:
34: Reading residue database... (Amber99sb-ildn)
34: Processing chain 1 (132 atoms, 16 residues)
34: Identified residue ALA34 as a starting terminus.
34: Identified residue ALA49 as a ending terminus.
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 16 residues with 255 atoms
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
34: The Amber99sb-ildn force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/6 (479 ms)
34: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/7
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 22 donors and 21 acceptors were found.
34: There are 30 hydrogen bonds
34: Will use HISE for residue 60
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: HIS60
34: NE285
34: CYS62 SG98 0.803
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34:
34: WARNING: Duplicate line found in or between hackblock and rtp entries
34:
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
34: Making bonds...
34: Number of bonds was 233, now 232
34: Marked 111 virtual sites
34: Added 18 dummy masses
34: Added 31 new constraints
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 603 pairs
34: Before cleaning: 634 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 634 dihedrals, 48 impropers, 419 angles
34: 597 pairs, 232 bonds and 116 virtual sites
34: Total mass 1662.888 a.m.u.
34: Total charge 0.000 e
34: Writing topology
34:
34: Writing coordinate file...
34:
34: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
34:
34: going to rename amber99sb-ildn.ff/aminoacids.r2b
34: going to rename amber99sb-ildn.ff/dna.r2b
34: going to rename amber99sb-ildn.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
34: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records or chain id changing.
34: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
34:
34: chain #res #atoms
34: 1 ' ' 16 117
34:
34: Reading residue database... (Amber99sb-ildn)
34: Processing chain 1 (117 atoms, 16 residues)
34: Identified residue LYS50 as a starting terminus.
34: Identified residue PRO65 as a ending terminus.
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 16 residues with 228 atoms
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
34: The Amber99sb-ildn force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/7 (423 ms)
34: [----------] 8 tests from ForAmber99sb_ildn/Pdb2gmxTest (3617 ms total)
34:
34: [----------] 8 tests from ForCharmm27/Pdb2gmxTest
34: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/0
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 25 donors and 23 acceptors were found.
34: There are 41 hydrogen bonds
34: Will use HISE for residue 8
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: CYS3 HIS8
34: SG9 NE251
34: HIS8 NE251 1.055
34: MET12 SD83 0.763 0.990
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 254, now 254
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 653 pairs
34: Before cleaning: 663 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 14 cmap torsion pairs
34: There are 663 dihedrals, 48 impropers, 457 angles
34: 650 pairs, 254 bonds and 0 virtual sites
34: Total mass 1846.115 a.m.u.
34: Total charge 0.000 e
34: Writing topology
34:
34: Writing coordinate file...
34:
34: Using the Charmm27 force field in directory charmm27.ff
34:
34: going to rename charmm27.ff/aminoacids.r2b
34: going to rename charmm27.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
34: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records or chain id changing.
34: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
34:
34: chain #res #atoms
34: 1 ' ' 16 128
34:
34: Reading residue database... (Charmm27)
34: Processing chain 1 (128 atoms, 16 residues)
34: Identified residue ALA2 as a starting terminus.
34: Identified residue SER17 as a ending terminus.
34: Start terminus ALA-2: NH3+
34: End terminus SER-17: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 16 residues with 252 atoms
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
34: The Charmm27 force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/0 (417 ms)
34: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/1
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 30 donors and 22 acceptors were found.
34: There are 36 hydrogen bonds
34: Will use HISE for residue 29
34: Will use HISE for residue 32
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: CYS27 HIS29
34: SG90 NE2111
34: HIS29 NE2111 0.987
34: HIS32 NE2135 1.590 1.155
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 290, now 290
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 748 pairs
34: Before cleaning: 778 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 14 cmap torsion pairs
34: There are 778 dihedrals, 49 impropers, 516 angles
34: 736 pairs, 290 bonds and 0 virtual sites
34: Total mass 2088.361 a.m.u.
34: Total charge 1.000 e
34: Writing topology
34:
34: Writing coordinate file...
34:
34: Using the Charmm27 force field in directory charmm27.ff
34:
34: going to rename charmm27.ff/aminoacids.r2b
34: going to rename charmm27.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
34: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records or chain id changing.
34: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
34:
34: chain #res #atoms
34: 1 ' ' 16 149
34:
34: Reading residue database... (Charmm27)
34: Processing chain 1 (149 atoms, 16 residues)
34: Identified residue THR18 as a starting terminus.
34: Identified residue PHE33 as a ending terminus.
34: Start terminus THR-18: NH3+
34: End terminus PHE-33: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 16 residues with 281 atoms
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
34: The Charmm27 force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/1 (476 ms)
34: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/2
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 22 donors and 22 acceptors were found.
34: There are 26 hydrogen bonds
34: Will use HISE for residue 45
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: HIS45
34: NE295
34: MET46 SD102 1.078
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 261, now 261
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 676 pairs
34: Before cleaning: 696 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 14 cmap torsion pairs
34: There are 696 dihedrals, 39 impropers, 472 angles
34: 667 pairs, 261 bonds and 0 virtual sites
34: Total mass 1861.130 a.m.u.
34: Total charge -1.000 e
34: Writing topology
34:
34: Writing coordinate file...
34:
34: Using the Charmm27 force field in directory charmm27.ff
34:
34: going to rename charmm27.ff/aminoacids.r2b
34: going to rename charmm27.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
34: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records or chain id changing.
34: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
34:
34: chain #res #atoms
34: 1 ' ' 16 132
34:
34: Reading residue database... (Charmm27)
34: Processing chain 1 (132 atoms, 16 residues)
34: Identified residue ALA34 as a starting terminus.
34: Identified residue ALA49 as a ending terminus.
34: Start terminus ALA-34: NH3+
34: End terminus ALA-49: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 16 residues with 255 atoms
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
34: The Charmm27 force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/2 (428 ms)
34: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/3
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 22 donors and 21 acceptors were found.
34: There are 30 hydrogen bonds
34: Will use HISE for residue 60
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: HIS60
34: NE285
34: CYS62 SG98 0.803
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 232, now 232
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 603 pairs
34: Before cleaning: 618 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 14 cmap torsion pairs
34: There are 618 dihedrals, 38 impropers, 419 angles
34: 597 pairs, 232 bonds and 0 virtual sites
34: Total mass 1662.885 a.m.u.
34: Total charge 0.000 e
34: Writing topology
34:
34: Writing coordinate file...
34:
34: Using the Charmm27 force field in directory charmm27.ff
34:
34: going to rename charmm27.ff/aminoacids.r2b
34: going to rename charmm27.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
34: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records or chain id changing.
34: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
34:
34: chain #res #atoms
34: 1 ' ' 16 117
34:
34: Reading residue database... (Charmm27)
34: Processing chain 1 (117 atoms, 16 residues)
34: Identified residue LYS50 as a starting terminus.
34: Identified residue PRO65 as a ending terminus.
34: Start terminus LYS-50: NH3+
34: End terminus PRO-65: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 16 residues with 228 atoms
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
34: The Charmm27 force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/3 (386 ms)
34: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/4
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 25 donors and 23 acceptors were found.
34: There are 41 hydrogen bonds
34: Will use HISE for residue 8
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: CYS3 HIS8
34: SG9 NE251
34: HIS8 NE251 1.055
34: MET12 SD83 0.763 0.990
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 254, now 254
34: Marked 124 virtual sites
34: Added 16 dummy masses
34: Added 26 new constraints
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 653 pairs
34: Before cleaning: 663 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 14 cmap torsion pairs
34: There are 663 dihedrals, 48 impropers, 457 angles
34: 650 pairs, 254 bonds and 130 virtual sites
34: Total mass 1846.115 a.m.u.
34: Total charge 0.000 e
34: Writing topology
34:
34: Writing coordinate file...
34:
34: Using the Charmm27 force field in directory charmm27.ff
34:
34: going to rename charmm27.ff/aminoacids.r2b
34: going to rename charmm27.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
34: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records or chain id changing.
34: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
34:
34: chain #res #atoms
34: 1 ' ' 16 128
34:
34: Reading residue database... (Charmm27)
34: Processing chain 1 (128 atoms, 16 residues)
34: Identified residue ALA2 as a starting terminus.
34: Identified residue SER17 as a ending terminus.
34: Start terminus ALA-2: NH3+
34: End terminus SER-17: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 16 residues with 252 atoms
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
34: The Charmm27 force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/4 (461 ms)
34: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/5
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 30 donors and 22 acceptors were found.
34: There are 36 hydrogen bonds
34: Will use HISE for residue 29
34: Will use HISE for residue 32
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: CYS27 HIS29
34: SG90 NE2111
34: HIS29 NE2111 0.987
34: HIS32 NE2135 1.590 1.155
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 290, now 290
34: Marked 132 virtual sites
34: Added 10 dummy masses
34: Added 19 new constraints
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 748 pairs
34: Before cleaning: 778 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 14 cmap torsion pairs
34: There are 778 dihedrals, 49 impropers, 516 angles
34: 736 pairs, 290 bonds and 133 virtual sites
34: Total mass 2088.361 a.m.u.
34: Total charge 1.000 e
34: Writing topology
34:
34: Writing coordinate file...
34:
34: Using the Charmm27 force field in directory charmm27.ff
34:
34: going to rename charmm27.ff/aminoacids.r2b
34: going to rename charmm27.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
34: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records or chain id changing.
34: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
34:
34: chain #res #atoms
34: 1 ' ' 16 149
34:
34: Reading residue database... (Charmm27)
34: Processing chain 1 (149 atoms, 16 residues)
34: Identified residue THR18 as a starting terminus.
34: Identified residue PHE33 as a ending terminus.
34: Start terminus THR-18: NH3+
34: End terminus PHE-33: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 16 residues with 281 atoms
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
34: The Charmm27 force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/5 (506 ms)
34: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/6
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 22 donors and 22 acceptors were found.
34: There are 26 hydrogen bonds
34: Will use HISE for residue 45
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: HIS45
34: NE295
34: MET46 SD102 1.078
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 261, now 261
34: Marked 123 virtual sites
34: Added 22 dummy masses
34: Added 35 new constraints
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 676 pairs
34: Before cleaning: 696 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 14 cmap torsion pairs
34: There are 696 dihedrals, 39 impropers, 472 angles
34: 667 pairs, 261 bonds and 132 virtual sites
34: Total mass 1861.130 a.m.u.
34: Total charge -1.000 e
34: Writing topology
34:
34: Writing coordinate file...
34:
34: Using the Charmm27 force field in directory charmm27.ff
34:
34: going to rename charmm27.ff/aminoacids.r2b
34: going to rename charmm27.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
34: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records or chain id changing.
34: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
34:
34: chain #res #atoms
34: 1 ' ' 16 132
34:
34: Reading residue database... (Charmm27)
34: Processing chain 1 (132 atoms, 16 residues)
34: Identified residue ALA34 as a starting terminus.
34: Identified residue ALA49 as a ending terminus.
34: Start terminus ALA-34: NH3+
34: End terminus ALA-49: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 16 residues with 255 atoms
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
34: The Charmm27 force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/6 (472 ms)
34: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/7
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 22 donors and 21 acceptors were found.
34: There are 30 hydrogen bonds
34: Will use HISE for residue 60
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: HIS60
34: NE285
34: CYS62 SG98 0.803
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 232, now 232
34: Marked 111 virtual sites
34: Added 18 dummy masses
34: Added 31 new constraints
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 603 pairs
34: Before cleaning: 618 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 14 cmap torsion pairs
34: There are 618 dihedrals, 38 impropers, 419 angles
34: 597 pairs, 232 bonds and 116 virtual sites
34: Total mass 1662.885 a.m.u.
34: Total charge 0.000 e
34: Writing topology
34:
34: Writing coordinate file...
34:
34: Using the Charmm27 force field in directory charmm27.ff
34:
34: going to rename charmm27.ff/aminoacids.r2b
34: going to rename charmm27.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
34: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records or chain id changing.
34: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
34:
34: chain #res #atoms
34: 1 ' ' 16 117
34:
34: Reading residue database... (Charmm27)
34: Processing chain 1 (117 atoms, 16 residues)
34: Identified residue LYS50 as a starting terminus.
34: Identified residue PRO65 as a ending terminus.
34: Start terminus LYS-50: NH3+
34: End terminus PRO-65: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 16 residues with 228 atoms
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
34: The Charmm27 force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/7 (423 ms)
34: [----------] 8 tests from ForCharmm27/Pdb2gmxTest (3569 ms total)
34:
34: [----------] 8 tests from ChainSep/Pdb2gmxTest
34: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/0
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 25 donors and 23 acceptors were found.
34: There are 41 hydrogen bonds
34: Will use HISE for residue 8
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: CYS3 HIS8
34: SG9 NE251
34: HIS8 NE251 1.055
34: MET12 SD83 0.763 0.990
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 258, now 258
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 651 pairs
34: Before cleaning: 661 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 10 cmap torsion pairs
34: There are 661 dihedrals, 46 impropers, 463 angles
34: 648 pairs, 258 bonds and 0 virtual sites
34: Total mass 1882.146 a.m.u.
34: Total charge 0.000 e
34: Writing topology
34:
34: Writing coordinate file...
34:
34: Using the Charmm27 force field in directory charmm27.ff
34:
34: going to rename charmm27.ff/aminoacids.r2b
34: going to rename charmm27.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
34: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on changing chain id only (ignoring TER records).
34:
34: Merged chains into joint molecule definitions at 2 places.
34:
34: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms
34:
34: chain #res #atoms
34: 1 'A' 16 127
34:
34: Reading residue database... (Charmm27)
34: Processing chain 1 'A' (127 atoms, 16 residues)
34: Identified residue ALA2 as a starting terminus.
34: Identified residue GLU5 as a ending terminus.
34: Identified residue PHE6 as a starting terminus.
34: Identified residue MET12 as a ending terminus.
34: Identified residue ASN13 as a starting terminus.
34: Identified residue SER17 as a ending terminus.
34: Start terminus ALA-2: NH3+
34: End terminus GLU-5: COO-
34: Start terminus PHE-6: NH3+
34: End terminus MET-12: COO-
34: Start terminus ASN-13: NH3+
34: End terminus SER-17: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 16 residues with 258 atoms
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
34: The Charmm27 force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/0 (437 ms)
34: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/1
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
34: 8 out of 8 lines of specbond.dat converted successfully
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 50, now 50
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 123 pairs
34: Before cleaning: 123 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 2 cmap torsion pairs
34: There are 123 dihedrals, 9 impropers, 88 angles
34: 123 pairs, 50 bonds and 0 virtual sites
34: Total mass 434.421 a.m.u.
34: Total charge -2.000 e
34: Writing topology
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 10 donors and 7 acceptors were found.
34: There are 7 hydrogen bonds
34: Will use HISE for residue 8
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: HIS8
34: NE223
34: MET12 SD55 0.990
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 125, now 125
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 317 pairs
34: Before cleaning: 322 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 5 cmap torsion pairs
34: There are 322 dihedrals, 19 impropers, 227 angles
34: 314 pairs, 125 bonds and 0 virtual sites
34: Total mass 846.083 a.m.u.
34: Total charge 1.000 e
34: Writing topology
34: 8 out of 8 lines of specbond.dat converted successfully
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 83, now 83
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 211 pairs
34: Before cleaning: 216 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 3 cmap torsion pairs
34: There are 216 dihedrals, 18 impropers, 148 angles
34: 211 pairs, 83 bonds and 0 virtual sites
34: Total mass 601.643 a.m.u.
34: Total charge 1.000 e
34: Writing topology
34: Now there are 258 atoms and 16 residues
34: Total mass in system 1882.146 a.m.u.
34: Total charge in system 0.000 e
34:
34: Writing coordinate file...
34:
34: Using the Charmm27 force field in directory charmm27.ff
34:
34: going to rename charmm27.ff/aminoacids.r2b
34: going to rename charmm27.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
34: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on changing chain id only (ignoring TER records).
34: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms
34:
34: chain #res #atoms
34: 1 'A' 4 28
34: 2 'B' 7 58
34: 3 'C' 5 41
34:
34: Reading residue database... (Charmm27)
34: Processing chain 1 'A' (28 atoms, 4 residues)
34: Identified residue ALA2 as a starting terminus.
34: Identified residue GLU5 as a ending terminus.
34: Start terminus ALA-2: NH3+
34: End terminus GLU-5: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 4 residues with 51 atoms
34: Chain time...
34: Processing chain 2 'B' (58 atoms, 7 residues)
34: Identified residue PHE6 as a starting terminus.
34: Identified residue MET12 as a ending terminus.
34: Start terminus PHE-6: NH3+
34: End terminus MET-12: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 7 residues with 124 atoms
34: Chain time...
34: Processing chain 3 'C' (41 atoms, 5 residues)
34: Identified residue ASN13 as a starting terminus.
34: Identified residue SER17 as a ending terminus.
34: Start terminus ASN-13: NH3+
34: End terminus SER-17: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 5 residues with 83 atoms
34: Chain time...
34: Including chain 1 in system: 51 atoms 4 residues
34: Including chain 2 in system: 124 atoms 7 residues
34: Including chain 3 in system: 83 atoms 5 residues
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
34: The Charmm27 force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/1 (300 ms)
34: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/2
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 25 donors and 23 acceptors were found.
34: There are 41 hydrogen bonds
34: Will use HISE for residue 8
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: CYS3 HIS8
34: SG9 NE251
34: HIS8 NE251 1.055
34: MET12 SD83 0.763 0.990
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 258, now 258
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 651 pairs
34: Before cleaning: 661 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 10 cmap torsion pairs
34: There are 661 dihedrals, 46 impropers, 463 angles
34: 648 pairs, 258 bonds and 0 virtual sites
34: Total mass 1882.146 a.m.u.
34: Total charge 0.000 e
34: Writing topology
34:
34: Writing coordinate file...
34:
34: Using the Charmm27 force field in directory charmm27.ff
34:
34: going to rename charmm27.ff/aminoacids.r2b
34: going to rename charmm27.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
34: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records only (ignoring chain id).
34:
34: Merged chains into joint molecule definitions at 2 places.
34:
34: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms
34:
34: chain #res #atoms
34: 1 'A' 16 127
34:
34: Reading residue database... (Charmm27)
34: Processing chain 1 'A' (127 atoms, 16 residues)
34: Identified residue ALA2 as a starting terminus.
34: Identified residue ILE9 as a ending terminus.
34: Identified residue LYS10 as a starting terminus.
34: Identified residue MET12 as a ending terminus.
34: Identified residue ASN13 as a starting terminus.
34: Identified residue SER17 as a ending terminus.
34: Start terminus ALA-2: NH3+
34: End terminus ILE-9: COO-
34: Start terminus LYS-10: NH3+
34: End terminus MET-12: COO-
34: Start terminus ASN-13: NH3+
34: End terminus SER-17: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 16 residues with 258 atoms
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
34: The Charmm27 force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/2 (435 ms)
34: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/3
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 10 donors and 12 acceptors were found.
34: There are 13 hydrogen bonds
34: Will use HISE for residue 8
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: CYS3
34: SG9
34: HIS8 NE251 1.055
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 115, now 115
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 288 pairs
34: Before cleaning: 293 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 6 cmap torsion pairs
34: There are 293 dihedrals, 23 impropers, 203 angles
34: 285 pairs, 115 bonds and 0 virtual sites
34: Total mass 888.952 a.m.u.
34: Total charge -2.000 e
34: Writing topology
34: 8 out of 8 lines of specbond.dat converted successfully
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 60, now 60
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 152 pairs
34: Before cleaning: 152 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 1 cmap torsion pairs
34: There are 152 dihedrals, 5 impropers, 112 angles
34: 152 pairs, 60 bonds and 0 virtual sites
34: Total mass 391.552 a.m.u.
34: Total charge 1.000 e
34: Writing topology
34: 8 out of 8 lines of specbond.dat converted successfully
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 83, now 83
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 211 pairs
34: Before cleaning: 216 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 3 cmap torsion pairs
34: There are 216 dihedrals, 18 impropers, 148 angles
34: 211 pairs, 83 bonds and 0 virtual sites
34: Total mass 601.643 a.m.u.
34: Total charge 1.000 e
34: Writing topology
34: Now there are 258 atoms and 16 residues
34: Total mass in system 1882.146 a.m.u.
34: Total charge in system 0.000 e
34:
34: Writing coordinate file...
34:
34: Using the Charmm27 force field in directory charmm27.ff
34:
34: going to rename charmm27.ff/aminoacids.r2b
34: going to rename charmm27.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
34: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records only (ignoring chain id).
34: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms
34:
34: chain #res #atoms
34: 1 'A' 8 61
34: 2 'B' 3 25
34: 3 'C' 5 41
34:
34: Reading residue database... (Charmm27)
34: Processing chain 1 'A' (61 atoms, 8 residues)
34: Identified residue ALA2 as a starting terminus.
34: Identified residue ILE9 as a ending terminus.
34: Start terminus ALA-2: NH3+
34: End terminus ILE-9: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 8 residues with 114 atoms
34: Chain time...
34: Processing chain 2 'B' (25 atoms, 3 residues)
34: Identified residue LYS10 as a starting terminus.
34: Identified residue MET12 as a ending terminus.
34: Start terminus LYS-10: NH3+
34: End terminus MET-12: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 3 residues with 61 atoms
34: Chain time...
34: Processing chain 3 'C' (41 atoms, 5 residues)
34: Identified residue ASN13 as a starting terminus.
34: Identified residue SER17 as a ending terminus.
34: Start terminus ASN-13: NH3+
34: End terminus SER-17: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 5 residues with 83 atoms
34: Chain time...
34: Including chain 1 in system: 114 atoms 8 residues
34: Including chain 2 in system: 61 atoms 3 residues
34: Including chain 3 in system: 83 atoms 5 residues
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
34: The Charmm27 force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/3 (296 ms)
34: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/4
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 25 donors and 23 acceptors were found.
34: There are 41 hydrogen bonds
34: Will use HISE for residue 8
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: CYS3 HIS8
34: SG9 NE251
34: HIS8 NE251 1.055
34: MET12 SD83 0.763 0.990
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 260, now 260
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 650 pairs
34: Before cleaning: 660 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 8 cmap torsion pairs
34: There are 660 dihedrals, 45 impropers, 466 angles
34: 647 pairs, 260 bonds and 0 virtual sites
34: Total mass 1900.162 a.m.u.
34: Total charge 0.000 e
34: Writing topology
34:
34: Writing coordinate file...
34:
34: Using the Charmm27 force field in directory charmm27.ff
34:
34: going to rename charmm27.ff/aminoacids.r2b
34: going to rename charmm27.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
34: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records or chain id changing.
34:
34: Merged chains into joint molecule definitions at 3 places.
34:
34: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms
34:
34: chain #res #atoms
34: 1 'A' 16 127
34:
34: Reading residue database... (Charmm27)
34: Processing chain 1 'A' (127 atoms, 16 residues)
34: Identified residue ALA2 as a starting terminus.
34: Identified residue GLU5 as a ending terminus.
34: Identified residue PHE6 as a starting terminus.
34: Identified residue ILE9 as a ending terminus.
34: Identified residue LYS10 as a starting terminus.
34: Identified residue MET12 as a ending terminus.
34: Identified residue ASN13 as a starting terminus.
34: Identified residue SER17 as a ending terminus.
34: Start terminus ALA-2: NH3+
34: End terminus GLU-5: COO-
34: Start terminus PHE-6: NH3+
34: End terminus ILE-9: COO-
34: Start terminus LYS-10: NH3+
34: End terminus MET-12: COO-
34: Start terminus ASN-13: NH3+
34: End terminus SER-17: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 16 residues with 261 atoms
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
34: The Charmm27 force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/4 (439 ms)
34: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/5
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
34: 8 out of 8 lines of specbond.dat converted successfully
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 50, now 50
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 123 pairs
34: Before cleaning: 123 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 2 cmap torsion pairs
34: There are 123 dihedrals, 9 impropers, 88 angles
34: 123 pairs, 50 bonds and 0 virtual sites
34: Total mass 434.421 a.m.u.
34: Total charge -2.000 e
34: Writing topology
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 6 donors and 4 acceptors were found.
34: There are 3 hydrogen bonds
34: Will use HISE for residue 8
34: 8 out of 8 lines of specbond.dat converted successfully
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 67, now 67
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 164 pairs
34: Before cleaning: 169 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 2 cmap torsion pairs
34: There are 169 dihedrals, 13 impropers, 118 angles
34: 161 pairs, 67 bonds and 0 virtual sites
34: Total mass 472.547 a.m.u.
34: Total charge 0.000 e
34: Writing topology
34: 8 out of 8 lines of specbond.dat converted successfully
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 60, now 60
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 152 pairs
34: Before cleaning: 152 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 1 cmap torsion pairs
34: There are 152 dihedrals, 5 impropers, 112 angles
34: 152 pairs, 60 bonds and 0 virtual sites
34: Total mass 391.552 a.m.u.
34: Total charge 1.000 e
34: Writing topology
34: 8 out of 8 lines of specbond.dat converted successfully
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 83, now 83
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 211 pairs
34: Before cleaning: 216 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 3 cmap torsion pairs
34: There are 216 dihedrals, 18 impropers, 148 angles
34: 211 pairs, 83 bonds and 0 virtual sites
34: Total mass 601.643 a.m.u.
34: Total charge 1.000 e
34: Writing topology
34: Now there are 261 atoms and 16 residues
34: Total mass in system 1900.162 a.m.u.
34: Total charge in system 0.000 e
34:
34: Writing coordinate file...
34:
34: Using the Charmm27 force field in directory charmm27.ff
34:
34: going to rename charmm27.ff/aminoacids.r2b
34: going to rename charmm27.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
34: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records or chain id changing.
34: WARNING: Chain identifier 'B' is used in two non-sequential blocks.
34: They will be treated as separate chains unless you reorder your file.
34: There are 4 chains and 0 blocks of water and 16 residues with 127 atoms
34:
34: chain #res #atoms
34: 1 'A' 4 28
34: 2 'B' 4 33
34: 3 'B' 3 25
34: 4 'C' 5 41
34:
34: Reading residue database... (Charmm27)
34: Processing chain 1 'A' (28 atoms, 4 residues)
34: Identified residue ALA2 as a starting terminus.
34: Identified residue GLU5 as a ending terminus.
34: Start terminus ALA-2: NH3+
34: End terminus GLU-5: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 4 residues with 51 atoms
34: Chain time...
34: Processing chain 2 'B' (33 atoms, 4 residues)
34: Identified residue PHE6 as a starting terminus.
34: Identified residue ILE9 as a ending terminus.
34: Start terminus PHE-6: NH3+
34: End terminus ILE-9: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 4 residues with 66 atoms
34: Chain time...
34: Processing chain 3 'B' (25 atoms, 3 residues)
34: Identified residue LYS10 as a starting terminus.
34: Identified residue MET12 as a ending terminus.
34: Start terminus LYS-10: NH3+
34: End terminus MET-12: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 3 residues with 61 atoms
34: Chain time...
34: Processing chain 4 'C' (41 atoms, 5 residues)
34: Identified residue ASN13 as a starting terminus.
34: Identified residue SER17 as a ending terminus.
34: Start terminus ASN-13: NH3+
34: End terminus SER-17: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 5 residues with 83 atoms
34: Chain time...
34: Including chain 1 in system: 51 atoms 4 residues
34: Including chain 2 in system: 66 atoms 4 residues
34: Including chain 3 in system: 61 atoms 3 residues
34: Including chain 4 in system: 83 atoms 5 residues
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
34: The Charmm27 force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/5 (297 ms)
34: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/6
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 25 donors and 23 acceptors were found.
34: There are 41 hydrogen bonds
34: Will use HISE for residue 8
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: CYS3 HIS8
34: SG9 NE251
34: HIS8 NE251 1.055
34: MET12 SD83 0.763 0.990
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 256, now 256
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 652 pairs
34: Before cleaning: 662 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 12 cmap torsion pairs
34: There are 662 dihedrals, 47 impropers, 460 angles
34: 649 pairs, 256 bonds and 0 virtual sites
34: Total mass 1864.131 a.m.u.
34: Total charge 0.000 e
34: Writing topology
34:
34: Writing coordinate file...
34:
34: Using the Charmm27 force field in directory charmm27.ff
34:
34: going to rename charmm27.ff/aminoacids.r2b
34: going to rename charmm27.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
34: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records and chain id changing.
34:
34: Merged chains into joint molecule definitions at 1 places.
34:
34: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms
34:
34: chain #res #atoms
34: 1 'A' 16 127
34:
34: Reading residue database... (Charmm27)
34: Processing chain 1 'A' (127 atoms, 16 residues)
34: Identified residue ALA2 as a starting terminus.
34: Identified residue MET12 as a ending terminus.
34: Identified residue ASN13 as a starting terminus.
34: Identified residue SER17 as a ending terminus.
34: Start terminus ALA-2: NH3+
34: End terminus MET-12: COO-
34: Start terminus ASN-13: NH3+
34: End terminus SER-17: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 16 residues with 255 atoms
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
34: The Charmm27 force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/6 (426 ms)
34: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/7
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
34: Analysing hydrogen-bonding network for automated assignment of histidine
34: protonation. 14 donors and 15 acceptors were found.
34: There are 20 hydrogen bonds
34: Will use HISE for residue 8
34: 8 out of 8 lines of specbond.dat converted successfully
34: Special Atom Distance matrix:
34: CYS3 HIS8
34: SG9 NE251
34: HIS8 NE251 1.055
34: MET12 SD83 0.763 0.990
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 173, now 173
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 441 pairs
34: Before cleaning: 446 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 9 cmap torsion pairs
34: There are 446 dihedrals, 29 impropers, 312 angles
34: 438 pairs, 173 bonds and 0 virtual sites
34: Total mass 1262.488 a.m.u.
34: Total charge -1.000 e
34: Writing topology
34: 8 out of 8 lines of specbond.dat converted successfully
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 83, now 83
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 211 pairs
34: Before cleaning: 216 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 3 cmap torsion pairs
34: There are 216 dihedrals, 18 impropers, 148 angles
34: 211 pairs, 83 bonds and 0 virtual sites
34: Total mass 601.643 a.m.u.
34: Total charge 1.000 e
34: Writing topology
34: Now there are 255 atoms and 16 residues
34: Total mass in system 1864.131 a.m.u.
34: Total charge in system 0.000 e
34:
34: Writing coordinate file...
34:
34: Using the Charmm27 force field in directory charmm27.ff
34:
34: going to rename charmm27.ff/aminoacids.r2b
34: going to rename charmm27.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
34: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records and chain id changing.
34: There are 2 chains and 0 blocks of water and 16 residues with 127 atoms
34:
34: chain #res #atoms
34: 1 'A' 11 86
34: 2 'C' 5 41
34:
34: Reading residue database... (Charmm27)
34: Processing chain 1 'A' (86 atoms, 11 residues)
34: Identified residue ALA2 as a starting terminus.
34: Identified residue MET12 as a ending terminus.
34: Start terminus ALA-2: NH3+
34: End terminus MET-12: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 11 residues with 172 atoms
34: Chain time...
34: Processing chain 2 'C' (41 atoms, 5 residues)
34: Identified residue ASN13 as a starting terminus.
34: Identified residue SER17 as a ending terminus.
34: Start terminus ASN-13: NH3+
34: End terminus SER-17: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 5 residues with 83 atoms
34: Chain time...
34: Including chain 1 in system: 172 atoms 11 residues
34: Including chain 2 in system: 83 atoms 5 residues
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
34: The Charmm27 force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/7 (314 ms)
34: [----------] 8 tests from ChainSep/Pdb2gmxTest (2944 ms total)
34:
34: [----------] 4 tests from ChainChanges/Pdb2gmxTest
34: [ RUN ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/0
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
34: 8 out of 8 lines of specbond.dat converted successfully
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 35, now 35
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 83 pairs
34: Before cleaning: 83 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 1 cmap torsion pairs
34: There are 83 dihedrals, 6 impropers, 61 angles
34: 83 pairs, 35 bonds and 0 virtual sites
34: Total mass 306.314 a.m.u.
34: Total charge -1.000 e
34: Writing topology
34: 8 out of 8 lines of specbond.dat converted successfully
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 58, now 58
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 145 pairs
34: Before cleaning: 150 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 1 cmap torsion pairs
34: There are 150 dihedrals, 5 impropers, 103 angles
34: 142 pairs, 58 bonds and 0 virtual sites
34: Total mass 404.468 a.m.u.
34: Total charge 0.000 e
34: Writing topology
34: Now there are 93 atoms and 6 residues
34: Total mass in system 710.782 a.m.u.
34: Total charge in system -1.000 e
34:
34: Writing coordinate file...
34:
34: Using the Charmm27 force field in directory charmm27.ff
34:
34: going to rename charmm27.ff/aminoacids.r2b
34: going to rename charmm27.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb...
34: Read 'Fragments of peptides and ions', 47 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on changing chain id only (ignoring TER records).
34: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms
34:
34: chain #res #atoms
34: 1 'A' 3 19
34: 2 'B' 3 28
34:
34: Reading residue database... (Charmm27)
34: Processing chain 1 'A' (19 atoms, 3 residues)
34: Identified residue ALA2 as a starting terminus.
34: Identified residue ASP4 as a ending terminus.
34: Start terminus ALA-2: NH3+
34: End terminus ASP-4: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 3 residues with 36 atoms
34: Chain time...
34: Processing chain 2 'B' (28 atoms, 3 residues)
34: Identified residue THR18 as a starting terminus.
34: Identified residue TRP20 as a ending terminus.
34: Start terminus THR-18: NH3+
34: End terminus TRP-20: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 3 residues with 57 atoms
34: Chain time...
34: Including chain 1 in system: 36 atoms 3 residues
34: Including chain 2 in system: 57 atoms 3 residues
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb.
34: The Charmm27 force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/0 (205 ms)
34: [ RUN ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/1
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
34: 8 out of 8 lines of specbond.dat converted successfully
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 35, now 35
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 83 pairs
34: Before cleaning: 83 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 1 cmap torsion pairs
34: There are 83 dihedrals, 6 impropers, 61 angles
34: 83 pairs, 35 bonds and 0 virtual sites
34: Total mass 306.314 a.m.u.
34: Total charge -1.000 e
34: Writing topology
34: 8 out of 8 lines of specbond.dat converted successfully
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 58, now 58
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 145 pairs
34: Before cleaning: 150 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 1 cmap torsion pairs
34: There are 150 dihedrals, 5 impropers, 103 angles
34: 142 pairs, 58 bonds and 0 virtual sites
34: Total mass 404.468 a.m.u.
34: Total charge 0.000 e
34: Writing topology
34: Now there are 93 atoms and 6 residues
34: Total mass in system 710.782 a.m.u.
34: Total charge in system -1.000 e
34:
34: Writing coordinate file...
34:
34: Using the Charmm27 force field in directory charmm27.ff
34:
34: going to rename charmm27.ff/aminoacids.r2b
34: going to rename charmm27.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb...
34: Read 'Fragments of peptides and ions', 47 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records only (ignoring chain id).
34: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms
34:
34: chain #res #atoms
34: 1 'A' 3 19
34: 2 'B' 3 28
34:
34: Reading residue database... (Charmm27)
34: Processing chain 1 'A' (19 atoms, 3 residues)
34: Identified residue ALA2 as a starting terminus.
34: Identified residue ASP4 as a ending terminus.
34: Start terminus ALA-2: NH3+
34: End terminus ASP-4: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 3 residues with 36 atoms
34: Chain time...
34: Processing chain 2 'B' (28 atoms, 3 residues)
34: Identified residue THR18 as a starting terminus.
34: Identified residue TRP20 as a ending terminus.
34: Start terminus THR-18: NH3+
34: End terminus TRP-20: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 3 residues with 57 atoms
34: Chain time...
34: Including chain 1 in system: 36 atoms 3 residues
34: Including chain 2 in system: 57 atoms 3 residues
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb.
34: The Charmm27 force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/1 (206 ms)
34: [ RUN ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/2
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
34: 8 out of 8 lines of specbond.dat converted successfully
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 35, now 35
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 83 pairs
34: Before cleaning: 83 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 1 cmap torsion pairs
34: There are 83 dihedrals, 6 impropers, 61 angles
34: 83 pairs, 35 bonds and 0 virtual sites
34: Total mass 306.314 a.m.u.
34: Total charge -1.000 e
34: Writing topology
34: 8 out of 8 lines of specbond.dat converted successfully
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 58, now 58
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 145 pairs
34: Before cleaning: 150 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 1 cmap torsion pairs
34: There are 150 dihedrals, 5 impropers, 103 angles
34: 142 pairs, 58 bonds and 0 virtual sites
34: Total mass 404.468 a.m.u.
34: Total charge 0.000 e
34: Writing topology
34: Now there are 93 atoms and 6 residues
34: Total mass in system 710.782 a.m.u.
34: Total charge in system -1.000 e
34:
34: Writing coordinate file...
34:
34: Using the Charmm27 force field in directory charmm27.ff
34:
34: going to rename charmm27.ff/aminoacids.r2b
34: going to rename charmm27.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb...
34: Read 'Fragments of peptides and ions', 47 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records or chain id changing.
34: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms
34:
34: chain #res #atoms
34: 1 'A' 3 19
34: 2 'B' 3 28
34:
34: Reading residue database... (Charmm27)
34: Processing chain 1 'A' (19 atoms, 3 residues)
34: Identified residue ALA2 as a starting terminus.
34: Identified residue ASP4 as a ending terminus.
34: Start terminus ALA-2: NH3+
34: End terminus ASP-4: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 3 residues with 36 atoms
34: Chain time...
34: Processing chain 2 'B' (28 atoms, 3 residues)
34: Identified residue THR18 as a starting terminus.
34: Identified residue TRP20 as a ending terminus.
34: Start terminus THR-18: NH3+
34: End terminus TRP-20: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 3 residues with 57 atoms
34: Chain time...
34: Including chain 1 in system: 36 atoms 3 residues
34: Including chain 2 in system: 57 atoms 3 residues
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb.
34: The Charmm27 force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/2 (206 ms)
34: [ RUN ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/3
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
34: All occupancies are one
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
34: 8 out of 8 lines of specbond.dat converted successfully
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 35, now 35
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 83 pairs
34: Before cleaning: 83 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 1 cmap torsion pairs
34: There are 83 dihedrals, 6 impropers, 61 angles
34: 83 pairs, 35 bonds and 0 virtual sites
34: Total mass 306.314 a.m.u.
34: Total charge -1.000 e
34: Writing topology
34: 8 out of 8 lines of specbond.dat converted successfully
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
34: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
34: Making bonds...
34: Number of bonds was 58, now 58
34: Generating angles, dihedrals and pairs...
34: Before cleaning: 145 pairs
34: Before cleaning: 150 dihedrals
34: Keeping all generated dihedrals
34: Making cmap torsions...
34: There are 1 cmap torsion pairs
34: There are 150 dihedrals, 5 impropers, 103 angles
34: 142 pairs, 58 bonds and 0 virtual sites
34: Total mass 404.468 a.m.u.
34: Total charge 0.000 e
34: Writing topology
34: Now there are 93 atoms and 6 residues
34: Total mass in system 710.782 a.m.u.
34: Total charge in system -1.000 e
34:
34: Writing coordinate file...
34:
34: Using the Charmm27 force field in directory charmm27.ff
34:
34: going to rename charmm27.ff/aminoacids.r2b
34: going to rename charmm27.ff/rna.r2b
34: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb...
34: Read 'Fragments of peptides and ions', 47 atoms
34: Analyzing pdb file
34: Splitting chemical chains based on TER records and chain id changing.
34: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms
34:
34: chain #res #atoms
34: 1 'A' 3 19
34: 2 'B' 3 28
34:
34: Reading residue database... (Charmm27)
34: Processing chain 1 'A' (19 atoms, 3 residues)
34: Identified residue ALA2 as a starting terminus.
34: Identified residue ASP4 as a ending terminus.
34: Start terminus ALA-2: NH3+
34: End terminus ASP-4: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 3 residues with 36 atoms
34: Chain time...
34: Processing chain 2 'B' (28 atoms, 3 residues)
34: Identified residue THR18 as a starting terminus.
34: Identified residue TRP20 as a ending terminus.
34: Start terminus THR-18: NH3+
34: End terminus TRP-20: COO-
34: Checking for duplicate atoms....
34: Generating any missing hydrogen atoms and/or adding termini.
34: Now there are 3 residues with 57 atoms
34: Chain time...
34: Including chain 1 in system: 36 atoms 3 residues
34: Including chain 2 in system: 57 atoms 3 residues
34: --------- PLEASE NOTE ------------
34: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb.
34: The Charmm27 force field and the tip3p water model are used.
34: --------- ETON ESAELP ------------
34: [ OK ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/3 (205 ms)
34: [----------] 4 tests from ChainChanges/Pdb2gmxTest (822 ms total)
34:
34: [----------] Global test environment tear-down
34: [==========] 28 tests from 4 test cases ran. (10953 ms total)
34: [ PASSED ] 28 tests.
34/52 Test #34: Pdb2gmx3Test ........................ Passed 11.02 sec
test 35
Start 35: CorrelationsTest
35: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/correlations-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/CorrelationsTest.xml"
35: Test timeout computed to be: 30
35: [==========] Running 21 tests from 3 test cases.
35: [----------] Global test environment set-up.
35: [----------] 10 tests from AutocorrTest
35: [ RUN ] AutocorrTest.EacNormal
35: [ OK ] AutocorrTest.EacNormal (19 ms)
35: [ RUN ] AutocorrTest.EacNoNormalize
35: [ OK ] AutocorrTest.EacNoNormalize (11 ms)
35: [ RUN ] AutocorrTest.EacCos
35: [ OK ] AutocorrTest.EacCos (17 ms)
35: [ RUN ] AutocorrTest.EacVector
35: [ OK ] AutocorrTest.EacVector (24 ms)
35: [ RUN ] AutocorrTest.EacRcross
35: [ OK ] AutocorrTest.EacRcross (8 ms)
35: [ RUN ] AutocorrTest.EacP0
35: [ OK ] AutocorrTest.EacP0 (24 ms)
35: [ RUN ] AutocorrTest.EacP1
35: [ OK ] AutocorrTest.EacP1 (24 ms)
35: [ RUN ] AutocorrTest.EacP2
35: [ OK ] AutocorrTest.EacP2 (44 ms)
35: [ RUN ] AutocorrTest.EacP3
35: [ OK ] AutocorrTest.EacP3 (21 ms)
35: [ RUN ] AutocorrTest.EacP4
35: [ OK ] AutocorrTest.EacP4 (24 ms)
35: [----------] 10 tests from AutocorrTest (224 ms total)
35:
35: [----------] 1 test from ManyAutocorrelationTest
35: [ RUN ] ManyAutocorrelationTest.Empty
35: [ OK ] ManyAutocorrelationTest.Empty (1 ms)
35: [----------] 1 test from ManyAutocorrelationTest (1 ms total)
35:
35: [----------] 10 tests from ExpfitTest
35: [ RUN ] ExpfitTest.EffnEXP1
35: [ OK ] ExpfitTest.EffnEXP1 (5 ms)
35: [ RUN ] ExpfitTest.EffnEXP2
35: [ OK ] ExpfitTest.EffnEXP2 (6 ms)
35: [ RUN ] ExpfitTest.EffnEXPEXP
35: [ OK ] ExpfitTest.EffnEXPEXP (13 ms)
35: [ RUN ] ExpfitTest.EffnEXP5
35: [ OK ] ExpfitTest.EffnEXP5 (39 ms)
35: [ RUN ] ExpfitTest.EffnEXP7
35: [ OK ] ExpfitTest.EffnEXP7 (39 ms)
35: [ RUN ] ExpfitTest.EffnEXP9
35: [ OK ] ExpfitTest.EffnEXP9 (149 ms)
35: [ RUN ] ExpfitTest.EffnERF
35: [ OK ] ExpfitTest.EffnERF (18 ms)
35: [ RUN ] ExpfitTest.EffnERREST
35: [ OK ] ExpfitTest.EffnERREST (7 ms)
35: [ RUN ] ExpfitTest.EffnVAC
35: [ OK ] ExpfitTest.EffnVAC (49 ms)
35: [ RUN ] ExpfitTest.EffnPRES
35: [ OK ] ExpfitTest.EffnPRES (103 ms)
35: [----------] 10 tests from ExpfitTest (429 ms total)
35:
35: [----------] Global test environment tear-down
35: [==========] 21 tests from 3 test cases ran. (709 ms total)
35: [ PASSED ] 21 tests.
35/52 Test #35: CorrelationsTest .................... Passed 0.77 sec
test 36
Start 36: AnalysisDataUnitTests
36: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/analysisdata-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/AnalysisDataUnitTests.xml"
36: Test timeout computed to be: 30
36: [==========] Running 69 tests from 14 test cases.
36: [----------] Global test environment set-up.
36: [----------] 3 tests from AnalysisDataInitializationTest
36: [ RUN ] AnalysisDataInitializationTest.BasicInitialization
36: [ OK ] AnalysisDataInitializationTest.BasicInitialization (1 ms)
36: [ RUN ] AnalysisDataInitializationTest.ChecksMultiColumnModules
36: [ OK ] AnalysisDataInitializationTest.ChecksMultiColumnModules (1 ms)
36: [ RUN ] AnalysisDataInitializationTest.ChecksMultipointModules
36: [ OK ] AnalysisDataInitializationTest.ChecksMultipointModules (0 ms)
36: [----------] 3 tests from AnalysisDataInitializationTest (2 ms total)
36:
36: [----------] 8 tests from AnalysisDataCommonTest/0, where TypeParam = (anonymous namespace)::SimpleInputData
36: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectly
36: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectly (4 ms)
36: [ RUN ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly
36: [ OK ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly (3 ms)
36: [ RUN ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly
36: [ OK ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly (3 ms)
36: [ RUN ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly
36: [ OK ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly (2 ms)
36: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames
36: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames (4 ms)
36: [ RUN ] AnalysisDataCommonTest/0.FullStorageWorks
36: [ OK ] AnalysisDataCommonTest/0.FullStorageWorks (1 ms)
36: [ RUN ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData
36: [ OK ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData (2 ms)
36: [ RUN ] AnalysisDataCommonTest/0.LimitedStorageWorks
36: [ OK ] AnalysisDataCommonTest/0.LimitedStorageWorks (1 ms)
36: [----------] 8 tests from AnalysisDataCommonTest/0 (22 ms total)
36:
36: [----------] 8 tests from AnalysisDataCommonTest/1, where TypeParam = (anonymous namespace)::DataSetsInputData
36: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectly
36: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectly (3 ms)
36: [ RUN ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly
36: [ OK ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly (3 ms)
36: [ RUN ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly
36: [ OK ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly (4 ms)
36: [ RUN ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly
36: [ OK ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly (3 ms)
36: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames
36: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames (5 ms)
36: [ RUN ] AnalysisDataCommonTest/1.FullStorageWorks
36: [ OK ] AnalysisDataCommonTest/1.FullStorageWorks (2 ms)
36: [ RUN ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData
36: [ OK ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData (2 ms)
36: [ RUN ] AnalysisDataCommonTest/1.LimitedStorageWorks
36: [ OK ] AnalysisDataCommonTest/1.LimitedStorageWorks (2 ms)
36: [----------] 8 tests from AnalysisDataCommonTest/1 (24 ms total)
36:
36: [----------] 8 tests from AnalysisDataCommonTest/2, where TypeParam = (anonymous namespace)::MultipointInputData
36: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectly
36: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectly (4 ms)
36: [ RUN ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly
36: [ OK ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly (4 ms)
36: [ RUN ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly
36: [ OK ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly (4 ms)
36: [ RUN ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly
36: [ OK ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly (3 ms)
36: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames
36: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames (6 ms)
36: [ RUN ] AnalysisDataCommonTest/2.FullStorageWorks
36: [ OK ] AnalysisDataCommonTest/2.FullStorageWorks (3 ms)
36: [ RUN ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData
36: [ OK ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData (2 ms)
36: [ RUN ] AnalysisDataCommonTest/2.LimitedStorageWorks
36: [ OK ] AnalysisDataCommonTest/2.LimitedStorageWorks (2 ms)
36: [----------] 8 tests from AnalysisDataCommonTest/2 (29 ms total)
36:
36: [----------] 8 tests from AnalysisDataCommonTest/3, where TypeParam = (anonymous namespace)::MultipointDataSetsInputData
36: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectly
36: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectly (4 ms)
36: [ RUN ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly
36: [ OK ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly (4 ms)
36: [ RUN ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly
36: [ OK ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly (4 ms)
36: [ RUN ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly
36: [ OK ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly (3 ms)
36: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames
36: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames (6 ms)
36: [ RUN ] AnalysisDataCommonTest/3.FullStorageWorks
36: [ OK ] AnalysisDataCommonTest/3.FullStorageWorks (2 ms)
36: [ RUN ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData
36: [ OK ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData (3 ms)
36: [ RUN ] AnalysisDataCommonTest/3.LimitedStorageWorks
36: [ OK ] AnalysisDataCommonTest/3.LimitedStorageWorks (2 ms)
36: [----------] 8 tests from AnalysisDataCommonTest/3 (29 ms total)
36:
36: [----------] 4 tests from AnalysisArrayDataTest
36: [ RUN ] AnalysisArrayDataTest.CallsModuleCorrectly
36: [ OK ] AnalysisArrayDataTest.CallsModuleCorrectly (3 ms)
36: [ RUN ] AnalysisArrayDataTest.StorageWorks
36: [ OK ] AnalysisArrayDataTest.StorageWorks (2 ms)
36: [ RUN ] AnalysisArrayDataTest.CanSetXAxis
36: [ OK ] AnalysisArrayDataTest.CanSetXAxis (0 ms)
36: [ RUN ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount
36: [ OK ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount (0 ms)
36: [----------] 4 tests from AnalysisArrayDataTest (6 ms total)
36:
36: [----------] 6 tests from AverageModuleTest
36: [ RUN ] AverageModuleTest.BasicTest
36: [ OK ] AverageModuleTest.BasicTest (4 ms)
36: [ RUN ] AverageModuleTest.HandlesMultipointData
36: [ OK ] AverageModuleTest.HandlesMultipointData (5 ms)
36: [ RUN ] AverageModuleTest.HandlesMultipleDataSets
36: [ OK ] AverageModuleTest.HandlesMultipleDataSets (6 ms)
36: [ RUN ] AverageModuleTest.HandlesDataSetAveraging
36: [ OK ] AverageModuleTest.HandlesDataSetAveraging (5 ms)
36: [ RUN ] AverageModuleTest.CanCustomizeXAxis
36: [ OK ] AverageModuleTest.CanCustomizeXAxis (4 ms)
36: [ RUN ] AverageModuleTest.CanCustomizeNonUniformXAxis
36: [ OK ] AverageModuleTest.CanCustomizeNonUniformXAxis (4 ms)
36: [----------] 6 tests from AverageModuleTest (29 ms total)
36:
36: [----------] 2 tests from FrameAverageModuleTest
36: [ RUN ] FrameAverageModuleTest.BasicTest
36: [ OK ] FrameAverageModuleTest.BasicTest (4 ms)
36: [ RUN ] FrameAverageModuleTest.HandlesMultipleDataSets
36: [ OK ] FrameAverageModuleTest.HandlesMultipleDataSets (6 ms)
36: [----------] 2 tests from FrameAverageModuleTest (10 ms total)
36:
36: [----------] 7 tests from AnalysisHistogramSettingsTest
36: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBins
36: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBins (0 ms)
36: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins
36: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins (0 ms)
36: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount
36: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount (0 ms)
36: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth
36: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth (0 ms)
36: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins
36: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins (0 ms)
36: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins
36: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins (0 ms)
36: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange
36: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange (0 ms)
36: [----------] 7 tests from AnalysisHistogramSettingsTest (0 ms total)
36:
36: [----------] 2 tests from SimpleHistogramModuleTest
36: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectly
36: [ OK ] SimpleHistogramModuleTest.ComputesCorrectly (6 ms)
36: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll
36: [ OK ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll (6 ms)
36: [----------] 2 tests from SimpleHistogramModuleTest (14 ms total)
36:
36: [----------] 3 tests from WeightedHistogramModuleTest
36: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectly
36: [ OK ] WeightedHistogramModuleTest.ComputesCorrectly (7 ms)
36: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll
36: [ OK ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll (7 ms)
36: [ RUN ] WeightedHistogramModuleTest.HandlesMultipleDataSets
36: [ OK ] WeightedHistogramModuleTest.HandlesMultipleDataSets (8 ms)
36: [----------] 3 tests from WeightedHistogramModuleTest (22 ms total)
36:
36: [----------] 3 tests from BinAverageModuleTest
36: [ RUN ] BinAverageModuleTest.ComputesCorrectly
36: [ OK ] BinAverageModuleTest.ComputesCorrectly (6 ms)
36: [ RUN ] BinAverageModuleTest.ComputesCorrectlyWithAll
36: [ OK ] BinAverageModuleTest.ComputesCorrectlyWithAll (6 ms)
36: [ RUN ] BinAverageModuleTest.HandlesMultipleDataSets
36: [ OK ] BinAverageModuleTest.HandlesMultipleDataSets (6 ms)
36: [----------] 3 tests from BinAverageModuleTest (18 ms total)
36:
36: [----------] 4 tests from AbstractAverageHistogramTest
36: [ RUN ] AbstractAverageHistogramTest.ClonesCorrectly
36: [ OK ] AbstractAverageHistogramTest.ClonesCorrectly (9 ms)
36: [ RUN ] AbstractAverageHistogramTest.ComputesCumulativeHistogram
36: [ OK ] AbstractAverageHistogramTest.ComputesCumulativeHistogram (7 ms)
36: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth
36: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth (6 ms)
36: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins
36: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins (7 ms)
36: [----------] 4 tests from AbstractAverageHistogramTest (29 ms total)
36:
36: [----------] 3 tests from LifetimeModuleTest
36: [ RUN ] LifetimeModuleTest.BasicTest
36: [ OK ] LifetimeModuleTest.BasicTest (4 ms)
36: [ RUN ] LifetimeModuleTest.CumulativeTest
36: [ OK ] LifetimeModuleTest.CumulativeTest (4 ms)
36: [ RUN ] LifetimeModuleTest.HandlesMultipleDataSets
36: [ OK ] LifetimeModuleTest.HandlesMultipleDataSets (4 ms)
36: [----------] 3 tests from LifetimeModuleTest (14 ms total)
36:
36: [----------] Global test environment tear-down
36: [==========] 69 tests from 14 test cases ran. (249 ms total)
36: [ PASSED ] 69 tests.
36/52 Test #36: AnalysisDataUnitTests ............... Passed 0.32 sec
test 37
Start 37: CoordinateIOTests
37: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/coordinateio-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/CoordinateIOTests.xml"
37: Test timeout computed to be: 30
37: [==========] Running 64 tests from 19 test cases.
37: [----------] Global test environment set-up.
37: [----------] 1 test from OutputSelectorDeathTest
37: [ RUN ] OutputSelectorDeathTest.RejectsBadSelection
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] OutputSelectorDeathTest.RejectsBadSelection (35 ms)
37: [----------] 1 test from OutputSelectorDeathTest (36 ms total)
37:
37: [----------] 5 tests from TrajectoryFrameWriterTest
37: [ RUN ] TrajectoryFrameWriterTest.RejectsWrongFiletype
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] TrajectoryFrameWriterTest.RejectsWrongFiletype (23 ms)
37: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms (22 ms)
37: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms (23 ms)
37: [ RUN ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms (44 ms)
37: [ RUN ] TrajectoryFrameWriterTest.TNGOutputWorks
37: [ OK ] TrajectoryFrameWriterTest.TNGOutputWorks (1 ms)
37: [----------] 5 tests from TrajectoryFrameWriterTest (113 ms total)
37:
37: [----------] 5 tests from OutputAdapterContainer
37: [ RUN ] OutputAdapterContainer.MakeEmpty
37: [ OK ] OutputAdapterContainer.MakeEmpty (0 ms)
37: [ RUN ] OutputAdapterContainer.AddAdapter
37: [ OK ] OutputAdapterContainer.AddAdapter (0 ms)
37: [ RUN ] OutputAdapterContainer.RejectBadAdapter
37: [ OK ] OutputAdapterContainer.RejectBadAdapter (0 ms)
37: [ RUN ] OutputAdapterContainer.RejectDuplicateAdapter
37: [ OK ] OutputAdapterContainer.RejectDuplicateAdapter (0 ms)
37: [ RUN ] OutputAdapterContainer.AcceptMultipleAdapters
37: [ OK ] OutputAdapterContainer.AcceptMultipleAdapters (0 ms)
37: [----------] 5 tests from OutputAdapterContainer (0 ms total)
37:
37: [----------] 5 tests from FlagTest
37: [ RUN ] FlagTest.CanSetSimpleFlag
37: [ OK ] FlagTest.CanSetSimpleFlag (0 ms)
37: [ RUN ] FlagTest.CanAddNewBox
37: [ OK ] FlagTest.CanAddNewBox (0 ms)
37: [ RUN ] FlagTest.SetsImplicitPrecisionChange
37: [ OK ] FlagTest.SetsImplicitPrecisionChange (0 ms)
37: [ RUN ] FlagTest.SetsImplicitStartTimeChange
37: [ OK ] FlagTest.SetsImplicitStartTimeChange (0 ms)
37: [ RUN ] FlagTest.SetsImplicitTimeStepChange
37: [ OK ] FlagTest.SetsImplicitTimeStepChange (0 ms)
37: [----------] 5 tests from FlagTest (1 ms total)
37:
37: [----------] 5 tests from SetAtomsTest
37: [ RUN ] SetAtomsTest.RemovesExistingAtoms
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] SetAtomsTest.RemovesExistingAtoms (23 ms)
37: [ RUN ] SetAtomsTest.AddsNewAtoms
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] SetAtomsTest.AddsNewAtoms (22 ms)
37: [ RUN ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable (22 ms)
37: [ RUN ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable (22 ms)
37: [ RUN ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible (22 ms)
37: [----------] 5 tests from SetAtomsTest (113 ms total)
37:
37: [----------] 2 tests from SetBothTimeTest
37: [ RUN ] SetBothTimeTest.StartTimeZeroWorks
37: [ OK ] SetBothTimeTest.StartTimeZeroWorks (0 ms)
37: [ RUN ] SetBothTimeTest.SetStartTimeNonZeroWorks
37: [ OK ] SetBothTimeTest.SetStartTimeNonZeroWorks (1 ms)
37: [----------] 2 tests from SetBothTimeTest (1 ms total)
37:
37: [----------] 2 tests from SetStartTimeTest
37: [ RUN ] SetStartTimeTest.WorksWithNonZeroStart
37: [ OK ] SetStartTimeTest.WorksWithNonZeroStart (0 ms)
37: [ RUN ] SetStartTimeTest.WorksWithZeroStart
37: [ OK ] SetStartTimeTest.WorksWithZeroStart (1 ms)
37: [----------] 2 tests from SetStartTimeTest (1 ms total)
37:
37: [----------] 1 test from SetTimeStepTest
37: [ RUN ] SetTimeStepTest.SetTimeStepWorks
37: [ OK ] SetTimeStepTest.SetTimeStepWorks (0 ms)
37: [----------] 1 test from SetTimeStepTest (0 ms total)
37:
37: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest
37: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0 (22 ms)
37: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1 (23 ms)
37: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2 (22 ms)
37: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3 (22 ms)
37: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4 (22 ms)
37: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5 (22 ms)
37: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest (134 ms total)
37:
37: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles
37: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/0
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/0 (22 ms)
37: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/1
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/1 (22 ms)
37: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/2
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/2 (22 ms)
37: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles (67 ms total)
37:
37: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles
37: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0
37: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0 (0 ms)
37: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1
37: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1 (0 ms)
37: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2
37: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2 (0 ms)
37: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles (1 ms total)
37:
37: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles
37: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/0
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/0 (44 ms)
37: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/1
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/1 (45 ms)
37: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/2
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/2 (45 ms)
37: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/3
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/3 (45 ms)
37: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles (181 ms total)
37:
37: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles
37: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/0
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/0 (22 ms)
37: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/1
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/1 (22 ms)
37: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/2
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/2 (22 ms)
37: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles (66 ms total)
37:
37: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles
37: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0
37: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0 (0 ms)
37: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1
37: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1 (0 ms)
37: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2
37: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2 (0 ms)
37: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles (1 ms total)
37:
37: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles
37: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/0
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/0 (22 ms)
37: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/1
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/1 (22 ms)
37: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles (44 ms total)
37:
37: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles
37: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0
37: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0 (0 ms)
37: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1
37: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1 (0 ms)
37: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2
37: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2 (0 ms)
37: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3
37: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3 (0 ms)
37: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles (1 ms total)
37:
37: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles
37: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/0
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/0 (22 ms)
37: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/1
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/1 (22 ms)
37: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles (44 ms total)
37:
37: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles
37: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0
37: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0 (0 ms)
37: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1
37: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1 (0 ms)
37: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2
37: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2 (1 ms)
37: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3
37: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3 (0 ms)
37: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles (1 ms total)
37:
37: [----------] 4 tests from ModuleSupported/NoOptionalOutput
37: [ RUN ] ModuleSupported/NoOptionalOutput.Works/0
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] ModuleSupported/NoOptionalOutput.Works/0 (22 ms)
37: [ RUN ] ModuleSupported/NoOptionalOutput.Works/1
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] ModuleSupported/NoOptionalOutput.Works/1 (22 ms)
37: [ RUN ] ModuleSupported/NoOptionalOutput.Works/2
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] ModuleSupported/NoOptionalOutput.Works/2 (22 ms)
37: [ RUN ] ModuleSupported/NoOptionalOutput.Works/3
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] ModuleSupported/NoOptionalOutput.Works/3 (22 ms)
37: [----------] 4 tests from ModuleSupported/NoOptionalOutput (88 ms total)
37:
37: [----------] Global test environment tear-down
37: [==========] 64 tests from 19 test cases ran. (896 ms total)
37: [ PASSED ] 64 tests.
37/52 Test #37: CoordinateIOTests ................... Passed 0.97 sec
test 38
Start 38: TrajectoryAnalysisUnitTests
38: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/trajectoryanalysis-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/TrajectoryAnalysisUnitTests.xml"
38: Test timeout computed to be: 30
38: [==========] Running 80 tests from 16 test cases.
38: [----------] Global test environment set-up.
38: [----------] 5 tests from ClustsizeTest
38: [ RUN ] ClustsizeTest.NoMolDefaultCutoff
38: Reading frames from pdb file
Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements
38: There is one group in the index
38: '', 24 atoms
38:
Reading frame 1 time 0.000
Last frame 1 time 0.000
38: Total number of atoms in clusters = 24
38: cmid: 2, cmax: 4, max_size: 6
38: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6
38: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolDefaultCutoff (15 ms)
38: [ RUN ] ClustsizeTest.NoMolShortCutoff
38: Reading frames from pdb file
Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements
38: There is one group in the index
38: '', 24 atoms
38:
Reading frame 1 time 0.000
Last frame 1 time 0.000
38: Total number of atoms in clusters = 24
38: cmid: 1, cmax: 6, max_size: 6
38: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6
38: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolShortCutoff (10 ms)
38: [ RUN ] ClustsizeTest.MolDefaultCutoff
38: Reading frames from pdb file
Reading frame 0 time 0.000 Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
38: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
38: '', 24 atoms
38:
Reading frame 1 time 0.000
Last frame 1 time 0.000
38: Total number of atoms in clusters = 8
38: cmid: 2, cmax: 4, max_size: 2
38: 50%100%cmid: 2, cmax: 6, max_size: 2
38: 50%100%[ OK ] ClustsizeTest.MolDefaultCutoff (13 ms)
38: [ RUN ] ClustsizeTest.MolShortCutoff
38: Reading frames from pdb file
Reading frame 0 time 0.000 Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
38: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
38: '', 24 atoms
38:
Reading frame 1 time 0.000
Last frame 1 time 0.000
38: Total number of atoms in clusters = 8
38: cmid: 1, cmax: 6, max_size: 2
38: 50%100%cmid: 2, cmax: 6, max_size: 2
38: 50%100%[ OK ] ClustsizeTest.MolShortCutoff (12 ms)
38: [ RUN ] ClustsizeTest.MolCSize
38: Reading frames from pdb file
Reading frame 0 time 0.000 Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
38: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
38: '', 24 atoms
38:
Reading frame 1 time 0.000
Last frame 1 time 0.000
38: Total number of atoms in clusters = 8
38: cmid: 2, cmax: 4, max_size: 2
38: 50%100%cmid: 2, cmax: 6, max_size: 2
38: 50%100%[ OK ] ClustsizeTest.MolCSize (13 ms)
38: [----------] 5 tests from ClustsizeTest (65 ms total)
38:
38: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest
38: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp
38: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp (5 ms)
38: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory
38: Reading frames from gro file 'Test system', 8 atoms.
38:
Reading frame 0 time 0.000
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38:
Reading frame 1 time 0.000
Last frame 1 time 0.000
38: Analyzed 2 frames, last time 0.000
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory (16 ms)
38: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset
38: Reading frames from gro file 'Test system', 8 atoms.
38:
Reading frame 0 time 0.000
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset (16 ms)
38: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory
38: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory (2 ms)
38: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest (39 ms total)
38:
38: [----------] 11 tests from AngleModuleTest
38: [ RUN ] AngleModuleTest.ComputesSimpleAngles
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] AngleModuleTest.ComputesSimpleAngles (18 ms)
38: [ RUN ] AngleModuleTest.ComputesDihedrals
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] AngleModuleTest.ComputesDihedrals (17 ms)
38: [ RUN ] AngleModuleTest.ComputesVectorPairAngles
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] AngleModuleTest.ComputesVectorPairAngles (18 ms)
38: [ RUN ] AngleModuleTest.ComputesVectorPlanePairAngles
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] AngleModuleTest.ComputesVectorPlanePairAngles (18 ms)
38: [ RUN ] AngleModuleTest.ComputesPlaneZAxisAngles
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] AngleModuleTest.ComputesPlaneZAxisAngles (17 ms)
38: [ RUN ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles (18 ms)
38: [ RUN ] AngleModuleTest.ComputesVectorTimeZeroAngles
38: Reading frames from gro file 'Test system for different angles', 33 atoms.
38:
Reading frame 0 time 0.000
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38:
Reading frame 1 time 0.000
Last frame 1 time 0.000
38: Analyzed 2 frames, last time 0.000
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] AngleModuleTest.ComputesVectorTimeZeroAngles (23 ms)
38: [ RUN ] AngleModuleTest.ComputesMultipleAngles
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] AngleModuleTest.ComputesMultipleAngles (19 ms)
38: [ RUN ] AngleModuleTest.HandlesDynamicSelections
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] AngleModuleTest.HandlesDynamicSelections (18 ms)
38: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorAngles
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorAngles (18 ms)
38: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles (18 ms)
38: [----------] 11 tests from AngleModuleTest (202 ms total)
38:
38: [----------] 4 tests from ConvertTrjModuleTest
38: [ RUN ] ConvertTrjModuleTest.WritesNormalOutput
38: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
38: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
38:
Reading frame 0 time 0.000
Last frame 0 time 0.000
38: Analyzed 1 frames, last time 0.000
38: [ OK ] ConvertTrjModuleTest.WritesNormalOutput (58 ms)
38: [ RUN ] ConvertTrjModuleTest.WritesAtomSubset
38: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
38: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
38:
Reading frame 0 time 0.000
Last frame 0 time 0.000
38: Analyzed 1 frames, last time 0.000
38: [ OK ] ConvertTrjModuleTest.WritesAtomSubset (63 ms)
38: [ RUN ] ConvertTrjModuleTest.WorksWithAtomAdding
38: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
38: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
38: Reading frames from pdb file
Reading frame 0 time 0.000 '', 24 atoms
38:
Reading frame 1 time 0.000
Last frame 1 time 0.000
38: Analyzed 2 frames, last time 0.000
38: [ OK ] ConvertTrjModuleTest.WorksWithAtomAdding (9 ms)
38: [ RUN ] ConvertTrjModuleTest.WorksWithAtomsAndSelection
38: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
38: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
38: Reading frames from pdb file
Reading frame 0 time 0.000 '', 24 atoms
38:
Reading frame 1 time 0.000
Last frame 1 time 0.000
38: Analyzed 2 frames, last time 0.000
38: [ OK ] ConvertTrjModuleTest.WorksWithAtomsAndSelection (9 ms)
38: [----------] 4 tests from ConvertTrjModuleTest (139 ms total)
38:
38: [----------] 3 tests from DistanceModuleTest
38: [ RUN ] DistanceModuleTest.ComputesDistances
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: atomname S1 S2:
38: Number of samples: 5
38: Average distance: 1.43246 nm
38: Standard deviation: 0.96700 nm
38: [ OK ] DistanceModuleTest.ComputesDistances (22 ms)
38: [ RUN ] DistanceModuleTest.ComputesMultipleDistances
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: atomname S1 S2:
38: Number of samples: 5
38: Average distance: 1.43246 nm
38: Standard deviation: 0.96700 nm
38: resindex 1 to 4 and atomname CB merge resindex 2 to 5 and atomname CB:
38: Number of samples: 4
38: Average distance: 1.81066 nm
38: Standard deviation: 0.79289 nm
38: [ OK ] DistanceModuleTest.ComputesMultipleDistances (25 ms)
38: [ RUN ] DistanceModuleTest.HandlesDynamicSelections
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: atomname S1 S2 and res_cog x < 2.8:
38: Number of samples: 3
38: Average distance: 1.72076 nm
38: Standard deviation: 1.24839 nm
38: [ OK ] DistanceModuleTest.HandlesDynamicSelections (23 ms)
38: [----------] 3 tests from DistanceModuleTest (70 ms total)
38:
38: [----------] 2 tests from ExtractClusterModuleTest
38: [ RUN ] ExtractClusterModuleTest.WorksWithAllAtoms
38: trr version: GMX_trn_file (single precision)
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.002
Reading frame 2 time 0.004
Reading frame 3 time 0.006
Reading frame 4 time 0.008
Reading frame 5 time 0.010
Reading frame 6 time 0.012
Reading frame 7 time 0.014
Reading frame 8 time 0.016
Reading frame 9 time 0.018
Reading frame 10 time 0.020
Reading frame 11 time 0.022
Reading frame 12 time 0.024
Reading frame 13 time 0.026
Reading frame 14 time 0.028
Reading frame 15 time 0.030
Reading frame 16 time 0.032
Reading frame 17 time 0.034
Reading frame 18 time 0.036
Reading frame 19 time 0.038
Reading frame 20 time 0.040
38: Analyzed 26 frames, last time 0.050
38: There are 8 clusters containing 26 structures, highest framenr is 25
38: [ OK ] ExtractClusterModuleTest.WorksWithAllAtoms (32 ms)
38: [ RUN ] ExtractClusterModuleTest.WorksWithAtomSubset
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.002
Reading frame 2 time 0.004
Reading frame 3 time 0.006
Reading frame 4 time 0.008
Reading frame 5 time 0.010
Reading frame 6 time 0.012
Reading frame 7 time 0.014
Reading frame 8 time 0.016
Reading frame 9 time 0.018
Reading frame 10 time 0.020
Reading frame 11 time 0.022
Reading frame 12 time 0.024
Reading frame 13 time 0.026
Reading frame 14 time 0.028
Reading frame 15 time 0.030
Reading frame 16 time 0.032
Reading frame 17 time 0.034
Reading frame 18 time 0.036
Reading frame 19 time 0.038
Reading frame 20 time 0.040
38: Analyzed 26 frames, last time 0.050
38: There are 8 clusters containing 26 structures, highest framenr is 25
38: [ OK ] ExtractClusterModuleTest.WorksWithAtomSubset (14 ms)
38: [----------] 2 tests from ExtractClusterModuleTest (47 ms total)
38:
38: [----------] 2 tests from FreeVolumeModuleTest
38: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolume
38: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
38: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
38: from the source below. This means the results may be different
38: compared to previous GROMACS versions.
38:
38: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
38: A. Bondi
38: van der Waals Volumes and Radii
38: J. Phys. Chem. 68 (1964) pp. 441-451
38: -------- -------- --- Thank You --- -------- --------
38:
38: Could not determine VDW radius for CO2-RM. Set to zero.
38: Could not determine VDW radius for CO2-RM. Set to zero.
38: Could not determine VDW radius for CO2-RM. Set to zero.
38: Could not determine VDW radius for CO2-RM. Set to zero.
38: Could not determine VDW radius for CO2-RM. Set to zero.
38: Could not determine VDW radius for CO2-RM. Set to zero.
38: Could not determine VDW radius for CO2-RM. Set to zero.
38: Could not determine VDW radius for CO2-RM. Set to zero.
38: Could not determine VDW radius for CO2-RM. Set to zero.
38: Could not determine VDW radius for 40 particles. These were set to zero.
38:
Reading frame 0 time 0.000
Last frame 0 time 0.000
38: Analyzed 1 frames, last time 0.000
38: cutoff = 0.18 nm
38: probe_radius = 0 nm
38: seed = 13
38: ninsert = 1000 probes per nm^3
38:
38: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
38: A. Bondi
38: van der Waals Volumes and Radii
38: J. Phys. Chem. 68 (1964) pp. 441-451
38: -------- -------- --- Thank You --- -------- --------
38:
38:
38: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
38: Tuanan C. Lourenco and Mariny F. C. Coelho and Teodorico C. Ramalho and David
38: van der Spoel and Luciano T. Costa
38: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium
38: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View
38: Environ. Sci. Technol. 47 (2013) pp. 7421-7429
38: -------- -------- --- Thank You --- -------- --------
38:
38: Free volume 38.02 +/- 0.00 %
38: Total volume 68.92 +/- 0.00 nm^3
38: Number of molecules 340 total mass 63491.38 Dalton
38: Average molar mass: 186.74 Dalton
38: Density rho: 1529.71 +/- 0.00 nm^3
38: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3
38: Molecular van der Waals volume assuming homogeneity: 0.1256 +/- 0.0000 nm^3
38: Fractional free volume 0.194 +/- 0.000
38: [ OK ] FreeVolumeModuleTest.ComputesFreeVolume (692 ms)
38: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolumeSelection
38: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
38: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
38: from the source below. This means the results may be different
38: compared to previous GROMACS versions.
38:
38: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
38: A. Bondi
38: van der Waals Volumes and Radii
38: J. Phys. Chem. 68 (1964) pp. 441-451
38: -------- -------- --- Thank You --- -------- --------
38:
38:
Reading frame 0 time 0.000
Last frame 0 time 0.000
38: Analyzed 1 frames, last time 0.000
38: cutoff = 0.18 nm
38: probe_radius = 0 nm
38: seed = 17
38: ninsert = 1000 probes per nm^3
38:
38: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
38: A. Bondi
38: van der Waals Volumes and Radii
38: J. Phys. Chem. 68 (1964) pp. 441-451
38: -------- -------- --- Thank You --- -------- --------
38:
38:
38: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
38: Tuanan C. Lourenco and Mariny F. C. Coelho and Teodorico C. Ramalho and David
38: van der Spoel and Luciano T. Costa
38: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium
38: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View
38: Environ. Sci. Technol. 47 (2013) pp. 7421-7429
38: -------- -------- --- Thank You --- -------- --------
38:
38: Free volume 38.48 +/- 0.00 %
38: Total volume 68.92 +/- 0.00 nm^3
38: Number of molecules 340 total mass 63491.38 Dalton
38: Average molar mass: 186.74 Dalton
38: Density rho: 1529.71 +/- 0.00 nm^3
38: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3
38: Molecular van der Waals volume assuming homogeneity: 0.1247 +/- 0.0000 nm^3
38: Fractional free volume 0.200 +/- 0.000
38: [ OK ] FreeVolumeModuleTest.ComputesFreeVolumeSelection (690 ms)
38: [----------] 2 tests from FreeVolumeModuleTest (1382 ms total)
38:
38: [----------] 7 tests from PairDistanceModuleTest
38: [ RUN ] PairDistanceModuleTest.ComputesAllDistances
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] PairDistanceModuleTest.ComputesAllDistances (18 ms)
38: [ RUN ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff (18 ms)
38: [ RUN ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff (18 ms)
38: [ RUN ] PairDistanceModuleTest.ComputesMaxDistance
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] PairDistanceModuleTest.ComputesMaxDistance (17 ms)
38: [ RUN ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff (18 ms)
38: [ RUN ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff (17 ms)
38: [ RUN ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff (17 ms)
38: [----------] 7 tests from PairDistanceModuleTest (124 ms total)
38:
38: [----------] 5 tests from RdfModuleTest
38: [ RUN ] RdfModuleTest.BasicTest
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] RdfModuleTest.BasicTest (153 ms)
38: [ RUN ] RdfModuleTest.SelectionsSolelyFromIndexFileWork
38: Reading frames from gro file '216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984', 648 atoms.
38:
Reading frame 0 time 0.000
Last frame 0 time 0.000
38: Analyzed 1 frames, last time 0.000
38: [ OK ] RdfModuleTest.SelectionsSolelyFromIndexFileWork (102 ms)
38: [ RUN ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork (153 ms)
38: [ RUN ] RdfModuleTest.CalculatesSurf
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] RdfModuleTest.CalculatesSurf (91 ms)
38: [ RUN ] RdfModuleTest.CalculatesXY
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] RdfModuleTest.CalculatesXY (173 ms)
38: [----------] 5 tests from RdfModuleTest (676 ms total)
38:
38: [----------] 5 tests from SasaModuleTest
38: [ RUN ] SasaModuleTest.BasicTest
38:
38: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
38: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
38: Michael Scharf
38: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
38: of Surface Area and Volume and to Dot Surface Contouring of Molecular
38: Assemblies
38: J. Comp. Chem. 16 (1995) pp. 273-284
38: -------- -------- --- Thank You --- -------- --------
38:
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
38: from the source below. This means the results may be different
38: compared to previous GROMACS versions.
38:
38: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
38: A. Bondi
38: van der Waals Volumes and Radii
38: J. Phys. Chem. 68 (1964) pp. 441-451
38: -------- -------- --- Thank You --- -------- --------
38:
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38: [ OK ] SasaModuleTest.BasicTest (78 ms)
38: [ RUN ] SasaModuleTest.HandlesSelectedResidues
38:
38: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
38: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
38: Michael Scharf
38: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
38: of Surface Area and Volume and to Dot Surface Contouring of Molecular
38: Assemblies
38: J. Comp. Chem. 16 (1995) pp. 273-284
38: -------- -------- --- Thank You --- -------- --------
38:
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
38: from the source below. This means the results may be different
38: compared to previous GROMACS versions.
38:
38: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
38: A. Bondi
38: van der Waals Volumes and Radii
38: J. Phys. Chem. 68 (1964) pp. 441-451
38: -------- -------- --- Thank You --- -------- --------
38:
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38: [ OK ] SasaModuleTest.HandlesSelectedResidues (48 ms)
38: [ RUN ] SasaModuleTest.WritesConnollySurfaceWithSolute
38:
38: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
38: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
38: Michael Scharf
38: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
38: of Surface Area and Volume and to Dot Surface Contouring of Molecular
38: Assemblies
38: J. Comp. Chem. 16 (1995) pp. 273-284
38: -------- -------- --- Thank You --- -------- --------
38:
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
38: from the source below. This means the results may be different
38: compared to previous GROMACS versions.
38:
38: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
38: A. Bondi
38: van der Waals Volumes and Radii
38: J. Phys. Chem. 68 (1964) pp. 441-451
38: -------- -------- --- Thank You --- -------- --------
38:
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38: [ OK ] SasaModuleTest.WritesConnollySurfaceWithSolute (41 ms)
38: [ RUN ] SasaModuleTest.HandlesDynamicOutputGroup
38:
38: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
38: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
38: Michael Scharf
38: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
38: of Surface Area and Volume and to Dot Surface Contouring of Molecular
38: Assemblies
38: J. Comp. Chem. 16 (1995) pp. 273-284
38: -------- -------- --- Thank You --- -------- --------
38:
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
38: from the source below. This means the results may be different
38: compared to previous GROMACS versions.
38:
38: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
38: A. Bondi
38: van der Waals Volumes and Radii
38: J. Phys. Chem. 68 (1964) pp. 441-451
38: -------- -------- --- Thank You --- -------- --------
38:
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38: [ OK ] SasaModuleTest.HandlesDynamicOutputGroup (57 ms)
38: [ RUN ] SasaModuleTest.HandlesDynamicCalculationGroup
38:
38: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
38: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
38: Michael Scharf
38: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
38: of Surface Area and Volume and to Dot Surface Contouring of Molecular
38: Assemblies
38: J. Comp. Chem. 16 (1995) pp. 273-284
38: -------- -------- --- Thank You --- -------- --------
38:
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
38: from the source below. This means the results may be different
38: compared to previous GROMACS versions.
38:
38: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
38: A. Bondi
38: van der Waals Volumes and Radii
38: J. Phys. Chem. 68 (1964) pp. 441-451
38: -------- -------- --- Thank You --- -------- --------
38:
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38: [ OK ] SasaModuleTest.HandlesDynamicCalculationGroup (55 ms)
38: [----------] 5 tests from SasaModuleTest (289 ms total)
38:
38: [----------] 8 tests from SelectModuleTest
38: [ RUN ] SelectModuleTest.BasicTest
38: Reading frames from gro file 'Test system', 15 atoms.
38:
Reading frame 0 time 0.000
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38:
Reading frame 1 time 0.000
Last frame 1 time 0.000
38: Analyzed 2 frames, last time 0.000
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] SelectModuleTest.BasicTest (33 ms)
38: [ RUN ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput
38: Reading frames from gro file 'Test system', 15 atoms.
38:
Reading frame 0 time 0.000
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38:
Reading frame 1 time 0.000
Last frame 1 time 0.000
38: Analyzed 2 frames, last time 0.000
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput (23 ms)
38: [ RUN ] SelectModuleTest.HandlesPDBOutputWithPDBInput
38: Reading frames from gro file 'Test system', 15 atoms.
38:
Reading frame 0 time 0.000
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38:
Reading frame 1 time 0.000
Last frame 1 time 0.000
38: Analyzed 2 frames, last time 0.000
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] SelectModuleTest.HandlesPDBOutputWithPDBInput (23 ms)
38: [ RUN ] SelectModuleTest.HandlesMaxPDBOutput
38: Reading frames from gro file 'Test system', 15 atoms.
38:
Reading frame 0 time 0.000
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38:
Reading frame 1 time 0.000
Last frame 1 time 0.000
38: Analyzed 2 frames, last time 0.000
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] SelectModuleTest.HandlesMaxPDBOutput (24 ms)
38: [ RUN ] SelectModuleTest.HandlesSelectedPDBOutput
38: Reading frames from gro file 'Test system', 15 atoms.
38:
Reading frame 0 time 0.000
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38:
Reading frame 1 time 0.000
Last frame 1 time 0.000
38: Analyzed 2 frames, last time 0.000
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] SelectModuleTest.HandlesSelectedPDBOutput (23 ms)
38: [ RUN ] SelectModuleTest.NormalizesSizes
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] SelectModuleTest.NormalizesSizes (17 ms)
38: [ RUN ] SelectModuleTest.WritesResidueNumbers
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] SelectModuleTest.WritesResidueNumbers (16 ms)
38: [ RUN ] SelectModuleTest.WritesResidueIndices
38:
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38: Analyzed topology coordinates
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] SelectModuleTest.WritesResidueIndices (17 ms)
38: [----------] 8 tests from SelectModuleTest (180 ms total)
38:
38: [----------] 10 tests from SurfaceAreaTest
38: [ RUN ] SurfaceAreaTest.ComputesSinglePoint
38: [ OK ] SurfaceAreaTest.ComputesSinglePoint (0 ms)
38: [ RUN ] SurfaceAreaTest.ComputesTwoPoints
38: [ OK ] SurfaceAreaTest.ComputesTwoPoints (7 ms)
38: [ RUN ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius
38: [ OK ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius (7 ms)
38: [ RUN ] SurfaceAreaTest.SurfacePoints12
38: [ OK ] SurfaceAreaTest.SurfacePoints12 (1 ms)
38: [ RUN ] SurfaceAreaTest.SurfacePoints32
38: [ OK ] SurfaceAreaTest.SurfacePoints32 (2 ms)
38: [ RUN ] SurfaceAreaTest.SurfacePoints42
38: [ OK ] SurfaceAreaTest.SurfacePoints42 (3 ms)
38: [ RUN ] SurfaceAreaTest.SurfacePoints122
38: [ OK ] SurfaceAreaTest.SurfacePoints122 (6 ms)
38: [ RUN ] SurfaceAreaTest.Computes100Points
38: [ OK ] SurfaceAreaTest.Computes100Points (4 ms)
38: [ RUN ] SurfaceAreaTest.Computes100PointsWithRectangularPBC
38: [ OK ] SurfaceAreaTest.Computes100PointsWithRectangularPBC (15 ms)
38: [ RUN ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC
38: [ OK ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC (17 ms)
38: [----------] 10 tests from SurfaceAreaTest (63 ms total)
38:
38: [----------] 4 tests from TopologyInformation
38: [ RUN ] TopologyInformation.CantWorkWithoutReadingAFile
38: [ OK ] TopologyInformation.CantWorkWithoutReadingAFile (0 ms)
38: [ RUN ] TopologyInformation.WorksWithGroFile
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] TopologyInformation.WorksWithGroFile (23 ms)
38: [ RUN ] TopologyInformation.WorksWithPdbFile
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] TopologyInformation.WorksWithPdbFile (22 ms)
38: [ RUN ] TopologyInformation.WorksWithTprFromPdbFile
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]:
38: For a correct single-point energy evaluation with nsteps = 0, use
38: continuation = yes to avoid constraining the input coordinates.
38:
38: Setting the LD random seed to -899231111
38: Generated 330891 of the 330891 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 330891 of the 330891 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
38:
38: NOTE 2 [file lysozyme.top, line 1465]:
38: System has non-zero total charge: 2.000000
38: Total charge should normally be an integer. See
38: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
38: for discussion on how close it should be to an integer.
38:
38:
38:
38: Number of degrees of freedom in T-Coupling group rest is 465.00
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]:
38: NVE simulation with an initial temperature of zero: will use a Verlet
38: buffer of 10%. Check your energy drift!
38:
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 4 notes
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
38: Analysing residue names:
38: There are: 10 Protein residues
38: Analysing Protein...
38: This run will generate roughly 0 Mb of data
38: [ OK ] TopologyInformation.WorksWithTprFromPdbFile (4482 ms)
38: [----------] 4 tests from TopologyInformation (4528 ms total)
38:
38: [----------] 4 tests from TrajectoryModuleTest
38: [ RUN ] TrajectoryModuleTest.BasicTest
38: Reading frames from gro file 'Test system', 15 atoms.
38:
Reading frame 0 time 0.000
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38:
Reading frame 1 time 0.000
Last frame 1 time 0.000
38: Analyzed 2 frames, last time 0.000
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] TrajectoryModuleTest.BasicTest (19 ms)
38: [ RUN ] TrajectoryModuleTest.PlotsXOnly
38: Reading frames from gro file 'Test system', 15 atoms.
38:
Reading frame 0 time 0.000
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38:
Reading frame 1 time 0.000
Last frame 1 time 0.000
38: Analyzed 2 frames, last time 0.000
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] TrajectoryModuleTest.PlotsXOnly (20 ms)
38: [ RUN ] TrajectoryModuleTest.HandlesNoVelocities
38: Reading frames from gro file 'Test system', 15 atoms.
38:
Reading frame 0 time 0.000
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38:
Reading frame 1 time 0.000
Last frame 1 time 0.000
38: Analyzed 2 frames, last time 0.000
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] TrajectoryModuleTest.HandlesNoVelocities (18 ms)
38: [ RUN ] TrajectoryModuleTest.HandlesNoForces
38: Reading frames from gro file 'Test system', 15 atoms.
38:
Reading frame 0 time 0.000
38: WARNING: If there are molecules in the input trajectory file
38: that are broken across periodic boundaries, they
38: cannot be made whole (or treated as whole) without
38: you providing a run input file.
38:
38:
Reading frame 1 time 0.000
Last frame 1 time 0.000
38: Analyzed 2 frames, last time 0.000
38:
38: WARNING: Masses and atomic (Van der Waals) radii will be guessed
38: based on residue and atom names, since they could not be
38: definitively assigned from the information in your input
38: files. These guessed numbers might deviate from the mass
38: and radius of the atom type. Please check the output
38: files if necessary.
38:
38: [ OK ] TrajectoryModuleTest.HandlesNoForces (18 ms)
38: [----------] 4 tests from TrajectoryModuleTest (75 ms total)
38:
38: [----------] 5 tests from UnionFinderTest
38: [ RUN ] UnionFinderTest.WorksEmpty
38: [ OK ] UnionFinderTest.WorksEmpty (0 ms)
38: [ RUN ] UnionFinderTest.BasicMerges
38: [ OK ] UnionFinderTest.BasicMerges (0 ms)
38: [ RUN ] UnionFinderTest.LargerMerges
38: [ OK ] UnionFinderTest.LargerMerges (0 ms)
38: [ RUN ] UnionFinderTest.LongRightMerge
38: [ OK ] UnionFinderTest.LongRightMerge (1 ms)
38: [ RUN ] UnionFinderTest.LongLeftMerge
38: [ OK ] UnionFinderTest.LongLeftMerge (0 ms)
38: [----------] 5 tests from UnionFinderTest (1 ms total)
38:
38: [----------] 1 test from MappedUnionFinderTest
38: [ RUN ] MappedUnionFinderTest.BasicMerges
38: [ OK ] MappedUnionFinderTest.BasicMerges (0 ms)
38: [----------] 1 test from MappedUnionFinderTest (0 ms total)
38:
38: [----------] Global test environment tear-down
38: [==========] 80 tests from 16 test cases ran. (7881 ms total)
38: [ PASSED ] 80 tests.
38/52 Test #38: TrajectoryAnalysisUnitTests ......... Passed 7.97 sec
test 39
Start 39: EnergyAnalysisUnitTests
39: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/energyanalysis-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/EnergyAnalysisUnitTests.xml"
39: Test timeout computed to be: 30
39: [==========] Running 7 tests from 4 test cases.
39: [----------] Global test environment set-up.
39: [----------] 1 test from DhdlTest
39: [ RUN ] DhdlTest.ExtractDhdl
39: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/dhdl.edr as double precision energy file
39: Reading file /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/dhdl.tpr, VERSION 2016-dev-20160810-e3ded7f (double precision)
39: Note: file tpx version 110, software tpx version 119
39:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.010
Reading energy frame 2 time 0.020
Reading energy frame 3 time 0.030
Reading energy frame 4 time 0.040
Reading energy frame 5 time 0.050
Reading energy frame 6 time 0.060
Reading energy frame 7 time 0.070
Reading energy frame 8 time 0.080
Reading energy frame 9 time 0.090
Reading energy frame 10 time 0.100
Reading energy frame 11 time 0.110
Reading energy frame 12 time 0.120
Reading energy frame 13 time 0.130
Reading energy frame 14 time 0.140
Reading energy frame 15 time 0.150
Reading energy frame 16 time 0.160
Reading energy frame 17 time 0.170
Reading energy frame 18 time 0.180
Reading energy frame 19 time 0.190
Reading energy frame 20 time 0.200
Reading energy frame 30 time 0.300
Reading energy frame 40 time 0.400
Reading energy frame 50 time 0.500
Reading energy frame 60 time 0.600
Reading energy frame 70 time 0.700
Reading energy frame 80 time 0.800
Reading energy frame 90 time 0.900
Reading energy frame 100 time 1.000
Last energy frame read 100 time 1.000
39:
39:
39: Wrote 8 lambda values with 101 samples as 808 dH data blocks to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/energyanalysis/tests/Testing/Temporary/DhdlTest_ExtractDhdl_dhdl.xvg
39: [ OK ] DhdlTest.ExtractDhdl (71 ms)
39: [----------] 1 test from DhdlTest (74 ms total)
39:
39: [----------] 1 test from OriresTest
39: [ RUN ] OriresTest.ExtractOrires
39: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/orires.edr as single precision energy file
39: Reading file /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/orires.tpr, VERSION 2017-dev-20170725-fea8651 (single precision)
39: Note: file tpx version 111, software tpx version 119
39: Found 7 orientation restraints with 1 experimentsSelect the orientation restraint labels you want (-1 is all)
39: End your selection with 0
39: Selecting all 7 orientation restraints
39:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.002
Reading energy frame 2 time 0.004
Reading energy frame 3 time 0.006
Reading energy frame 4 time 0.008
Reading energy frame 5 time 0.010
Reading energy frame 6 time 0.012
Reading energy frame 7 time 0.014
Reading energy frame 8 time 0.016
Reading energy frame 9 time 0.018
Reading energy frame 10 time 0.020
Last energy frame read 10 time 0.020
39: [ OK ] OriresTest.ExtractOrires (73 ms)
39: [----------] 1 test from OriresTest (74 ms total)
39:
39: [----------] 3 tests from EnergyTest
39: [ RUN ] EnergyTest.ExtractEnergy
39: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
39:
39: Select the terms you want from the following list by
39: selecting either (part of) the name or the number or a combination.
39: End your selection with an empty line or a zero.
39: -------------------------------------------------------------------
39: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip.
39: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature
39: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y
39: 13 Box-Z 14 Volume 15 Density 16 pV
39: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ
39: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX
39: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY
39: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ
39: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen
39: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System
39:
39:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
39:
39: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets
39: All statistics are over 5001 points
39:
39: Energy Average Err.Est. RMSD Tot-Drift
39: -------------------------------------------------------------------------------
39: Potential -34142.2 39 228.993 -62.8906 (kJ/mol)
39: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol)
39: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol)
39: [ OK ] EnergyTest.ExtractEnergy (15 ms)
39: [ RUN ] EnergyTest.ExtractEnergyByNumber
39: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
39:
39: Select the terms you want from the following list by
39: selecting either (part of) the name or the number or a combination.
39: End your selection with an empty line or a zero.
39: -------------------------------------------------------------------
39: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip.
39: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature
39: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y
39: 13 Box-Z 14 Volume 15 Density 16 pV
39: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ
39: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX
39: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY
39: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ
39: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen
39: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System
39:
39:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
39:
39: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets
39: All statistics are over 5001 points
39:
39: Energy Average Err.Est. RMSD Tot-Drift
39: -------------------------------------------------------------------------------
39: Coul. recip. 302.771 2.8 17.5152 12.5403 (kJ/mol)
39: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol)
39: Pres. DC -268.49 3 8.52175 13.2804 (bar)
39: [ OK ] EnergyTest.ExtractEnergyByNumber (15 ms)
39: [ RUN ] EnergyTest.ExtractEnergyMixed
39: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
39:
39: Select the terms you want from the following list by
39: selecting either (part of) the name or the number or a combination.
39: End your selection with an empty line or a zero.
39: -------------------------------------------------------------------
39: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip.
39: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature
39: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y
39: 13 Box-Z 14 Volume 15 Density 16 pV
39: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ
39: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX
39: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY
39: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ
39: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen
39: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System
39:
39:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
39:
39: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 4 data sets
39: All statistics are over 5001 points
39:
39: Energy Average Err.Est. RMSD Tot-Drift
39: -------------------------------------------------------------------------------
39: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol)
39: Pressure 5.34371 4.1 605.307 -4.88771 (bar)
39: Box-Z 2.92457 0.0054 0.0151558 0.0234974 (nm)
39: Volume 25.0162 0.14 0.386769 0.598615 (nm^3)
39: [ OK ] EnergyTest.ExtractEnergyMixed (18 ms)
39: [----------] 3 tests from EnergyTest (51 ms total)
39:
39: [----------] 2 tests from ViscosityTest
39: [ RUN ] ViscosityTest.EinsteinViscosity
39: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
39:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
39:
39: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets
39: All statistics are over 5001 points
39:
39: Energy Average Err.Est. RMSD Tot-Drift
39: -------------------------------------------------------------------------------
39: Pres-XX 20.2092 65 717.193 185.978 (bar)
39: Pres-XY -47.7351 39 372.522 207.456 (bar)
39: Pres-XZ 11.477 31 379.79 6.80818 (bar)
39: Pres-YX -47.7106 39 372.525 207.5 (bar)
39: Pres-YY 38.9241 40 803.899 -27.1505 (bar)
39: Pres-YZ -41.3534 45 401.216 114.663 (bar)
39: Pres-ZX 11.5238 31 379.804 6.91707 (bar)
39: Pres-ZY -41.3119 45 401.196 114.743 (bar)
39: Pres-ZZ -43.1021 63 748.522 -173.491 (bar)
39: Temperature 300.001 0.02 5.8425 -0.0130558 (K)
39: Volume 25.0162 0.14 0.386769 0.598615 (nm^3)
39: Pressure 5.34371 4.1 605.307 -4.88771 (bar)
39: [ OK ] ViscosityTest.EinsteinViscosity (34 ms)
39: [ RUN ] ViscosityTest.EinsteinViscosityIntegral
39: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
39:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
39:
39: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets
39: All statistics are over 5001 points
39:
39: Energy Average Err.Est. RMSD Tot-Drift
39: -------------------------------------------------------------------------------
39: Pres-XX 20.2092 65 717.193 185.978 (bar)
39: Pres-XY -47.7351 39 372.522 207.456 (bar)
39: Pres-XZ 11.477 31 379.79 6.80818 (bar)
39: Pres-YX -47.7106 39 372.525 207.5 (bar)
39: Pres-YY 38.9241 40 803.899 -27.1505 (bar)
39: Pres-YZ -41.3534 45 401.216 114.663 (bar)
39: Pres-ZX 11.5238 31 379.804 6.91707 (bar)
39: Pres-ZY -41.3119 45 401.196 114.743 (bar)
39: Pres-ZZ -43.1021 63 748.522 -173.491 (bar)
39: Temperature 300.001 0.02 5.8425 -0.0130558 (K)
39: Volume 25.0162 0.14 0.386769 0.598615 (nm^3)
39: Pressure 5.34371 4.1 605.307 -4.88771 (bar)
39: [ OK ] ViscosityTest.EinsteinViscosityIntegral (30 ms)
39: [----------] 2 tests from ViscosityTest (64 ms total)
39:
39: [----------] Global test environment tear-down
39: [==========] 7 tests from 4 test cases ran. (265 ms total)
39: [ PASSED ] 7 tests.
39/52 Test #39: EnergyAnalysisUnitTests ............. Passed 0.33 sec
test 40
Start 40: ToolUnitTests
40: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/tool-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/ToolUnitTests.xml"
40: Test timeout computed to be: 30
40: [==========] Running 18 tests from 4 test cases.
40: [----------] Global test environment set-up.
40: [----------] 2 tests from DumpTest
40:
40: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]:
40: For a correct single-point energy evaluation with nsteps = 0, use
40: continuation = yes to avoid constraining the input coordinates.
40:
40: Setting the LD random seed to 1996804239
40: Generated 330891 of the 330891 non-bonded parameter combinations
40: Generating 1-4 interactions: fudge = 0.5
40: Generated 330891 of the 330891 1-4 parameter combinations
40: Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
40:
40: NOTE 2 [file lysozyme.top, line 1465]:
40: System has non-zero total charge: 2.000000
40: Total charge should normally be an integer. See
40: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
40: for discussion on how close it should be to an integer.
40:
40:
40:
40: Number of degrees of freedom in T-Coupling group rest is 465.00
40:
40: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]:
40: NVE simulation with an initial temperature of zero: will use a Verlet
40: buffer of 10%. Check your energy drift!
40:
40:
40: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]:
40: You are using a plain Coulomb cut-off, which might produce artifacts.
40: You might want to consider using PME electrostatics.
40:
40:
40:
40: There were 4 notes
40: Analysing residue names:
40: There are: 10 Protein residues
40: Analysing Protein...
40: This run will generate roughly 0 Mb of data
40: [ RUN ] DumpTest.WorksWithTpr
40: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
40: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
40: /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr:
40: inputrec:
40: integrator = md
40: tinit = 0
40: dt = 0.001
40: nsteps = 0
40: init-step = 0
40: simulation-part = 1
40: comm-mode = Linear
40: nstcomm = 100
40: bd-fric = 0
40: ld-seed = 1996804239
40: emtol = 10
40: emstep = 0.01
40: niter = 20
40: fcstep = 0
40: nstcgsteep = 1000
40: nbfgscorr = 10
40: rtpi = 0.05
40: nstxout = 0
40: nstvout = 0
40: nstfout = 0
40: nstlog = 1000
40: nstcalcenergy = 100
40: nstenergy = 1000
40: nstxout-compressed = 0
40: compressed-x-precision = 1000
40: cutoff-scheme = Verlet
40: nstlist = 10
40: pbc = xyz
40: periodic-molecules = false
40: verlet-buffer-tolerance = -1
40: rlist = 1.1
40: coulombtype = Cut-off
40: coulomb-modifier = Potential-shift
40: rcoulomb-switch = 0
40: rcoulomb = 1
40: epsilon-r = 1
40: epsilon-rf = inf
40: vdw-type = Cut-off
40: vdw-modifier = Potential-shift
40: rvdw-switch = 0
40: rvdw = 1
40: DispCorr = No
40: table-extension = 1
40: fourierspacing = 0.12
40: fourier-nx = 0
40: fourier-ny = 0
40: fourier-nz = 0
40: pme-order = 4
40: ewald-rtol = 1e-05
40: ewald-rtol-lj = 0.001
40: lj-pme-comb-rule = Geometric
40: ewald-geometry = 0
40: epsilon-surface = 0
40: tcoupl = No
40: nsttcouple = -1
40: nh-chain-length = 0
40: print-nose-hoover-chain-variables = false
40: pcoupl = No
40: pcoupltype = Isotropic
40: nstpcouple = -1
40: tau-p = 1
40: compressibility (3x3):
40: compressibility[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: compressibility[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: compressibility[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: ref-p (3x3):
40: ref-p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: ref-p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: refcoord-scaling = No
40: posres-com (3):
40: posres-com[0]= 0.00000e+00
40: posres-com[1]= 0.00000e+00
40: posres-com[2]= 0.00000e+00
40: posres-comB (3):
40: posres-comB[0]= 0.00000e+00
40: posres-comB[1]= 0.00000e+00
40: posres-comB[2]= 0.00000e+00
40: QMMM = false
40: QMconstraints = 0
40: QMMMscheme = 0
40: MMChargeScaleFactor = 1
40: qm-opts:
40: ngQM = 0
40: constraint-algorithm = Lincs
40: continuation = false
40: Shake-SOR = false
40: shake-tol = 0.0001
40: lincs-order = 4
40: lincs-iter = 1
40: lincs-warnangle = 30
40: nwall = 0
40: wall-type = 9-3
40: wall-r-linpot = -1
40: wall-atomtype[0] = -1
40: wall-atomtype[1] = -1
40: wall-density[0] = 0
40: wall-density[1] = 0
40: wall-ewald-zfac = 3
40: pull = false
40: awh = false
40: rotation = false
40: interactiveMD = false
40: disre = No
40: disre-weighting = Conservative
40: disre-mixed = false
40: dr-fc = 1000
40: dr-tau = 0
40: nstdisreout = 100
40: orire-fc = 0
40: orire-tau = 0
40: nstorireout = 100
40: free-energy = no
40: cos-acceleration = 0
40: deform (3x3):
40: deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: simulated-tempering = false
40: swapcoords = no
40: userint1 = 0
40: userint2 = 0
40: userint3 = 0
40: userint4 = 0
40: userreal1 = 0
40: userreal2 = 0
40: userreal3 = 0
40: userreal4 = 0
40: applied-forces:
40: electric-field:
40: x:
40: E0 = 0
40: omega = 0
40: t0 = 0
40: sigma = 0
40: y:
40: E0 = 0
40: omega = 0
40: t0 = 0
40: sigma = 0
40: z:
40: E0 = 0
40: omega = 0
40: t0 = 0
40: sigma = 0
40: density-guided-simulation:
40: active = false
40: group = protein
40: similarity-measure = inner-product
40: atom-spreading-weight = unity
40: force-constant = 1e+09
40: gaussian-transform-spreading-width = 0.2
40: gaussian-transform-spreading-range-in-multiples-of-width = 4
40: reference-density-filename = reference.mrc
40: nst = 1
40: normalize-densities = true
40: adaptive-force-scaling = false
40: adaptive-force-scaling-time-constant = 4
40: grpopts:
40: nrdf: 465
40: ref-t: 0
40: tau-t: 0
40: annealing: No
40: annealing-npoints: 0
40: acc: 0 0 0
40: nfreeze: N N N
40: energygrp-flags[ 0]: 0
40: header:
40: bIr = present
40: bBox = present
40: bTop = present
40: bX = present
40: bV = present
40: bF = not present
40: natoms = 156
40: lambda = 0.000000e+00
40: buffer size = 70122
40: topology:
40: name="First 10 residues from 1AKI"
40: #atoms = 156
40: #molblock = 1
40: molblock (0):
40: moltype = 0 "Protein_chain_B"
40: #molecules = 1
40: #posres_xA = 0
40: #posres_xB = 0
40: bIntermolecularInteractions = false
40: ffparams:
40: atnr=10
40: ntypes=212
40: functype[0]=LJ_SR, c6= 3.35274678e-03, c12= 3.95094442e-06
40: functype[1]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
40: functype[2]=LJ_SR, c6= 2.60916961e-03, c12= 3.84022374e-06
40: functype[3]=LJ_SR, c6= 6.41072082e-04, c12= 3.43856290e-07
40: functype[4]=LJ_SR, c6= 4.04775915e-03, c12= 7.32754594e-06
40: functype[5]=LJ_SR, c6= 2.81521126e-03, c12= 2.50631820e-06
40: functype[6]=LJ_SR, c6= 2.80388560e-03, c12= 4.30621225e-06
40: functype[7]=LJ_SR, c6= 5.81477529e-04, c12= 2.82897505e-07
40: functype[8]=LJ_SR, c6= 6.03335344e-04, c12= 2.35915461e-07
40: functype[9]=LJ_SR, c6= 7.20490366e-03, c12= 1.15394674e-05
40: functype[10]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
40: functype[11]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
40: functype[12]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
40: functype[13]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
40: functype[14]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
40: functype[15]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
40: functype[16]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
40: functype[17]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
40: functype[18]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
40: functype[19]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
40: functype[20]=LJ_SR, c6= 2.60916961e-03, c12= 3.84022374e-06
40: functype[21]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
40: functype[22]=LJ_SR, c6= 2.03050409e-03, c12= 3.73260587e-06
40: functype[23]=LJ_SR, c6= 4.98894161e-04, c12= 3.34220112e-07
40: functype[24]=LJ_SR, c6= 3.15004110e-03, c12= 7.12219987e-06
40: functype[25]=LJ_SR, c6= 2.19084952e-03, c12= 2.43608151e-06
40: functype[26]=LJ_SR, c6= 2.18203568e-03, c12= 4.18553559e-06
40: functype[27]=LJ_SR, c6= 4.52516577e-04, c12= 2.74969627e-07
40: functype[28]=LJ_SR, c6= 4.69526733e-04, c12= 2.29304201e-07
40: functype[29]=LJ_SR, c6= 5.60698940e-03, c12= 1.12160870e-05
40: functype[30]=LJ_SR, c6= 6.41072082e-04, c12= 3.43856290e-07
40: functype[31]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
40: functype[32]=LJ_SR, c6= 4.98894161e-04, c12= 3.34220112e-07
40: functype[33]=LJ_SR, c6= 1.22578125e-04, c12= 2.99263000e-08
40: functype[34]=LJ_SR, c6= 7.73964023e-04, c12= 6.37726703e-07
40: functype[35]=LJ_SR, c6= 5.38290978e-04, c12= 2.18128423e-07
40: functype[36]=LJ_SR, c6= 5.36125420e-04, c12= 3.74775753e-07
40: functype[37]=LJ_SR, c6= 1.11183168e-04, c12= 2.46209706e-08
40: functype[38]=LJ_SR, c6= 1.15362558e-04, c12= 2.05320568e-08
40: functype[39]=LJ_SR, c6= 1.37763538e-03, c12= 1.00429619e-06
40: functype[40]=LJ_SR, c6= 4.04775915e-03, c12= 7.32754594e-06
40: functype[41]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
40: functype[42]=LJ_SR, c6= 3.15004110e-03, c12= 7.12219987e-06
40: functype[43]=LJ_SR, c6= 7.73964023e-04, c12= 6.37726703e-07
40: functype[44]=LJ_SR, c6= 4.88684509e-03, c12= 1.35898974e-05
40: functype[45]=LJ_SR, c6= 3.39879445e-03, c12= 4.64829665e-06
40: functype[46]=LJ_SR, c6= 3.38512102e-03, c12= 7.98643684e-06
40: functype[47]=LJ_SR, c6= 7.02015733e-04, c12= 5.24670621e-07
40: functype[48]=LJ_SR, c6= 7.28404594e-04, c12= 4.37536244e-07
40: functype[49]=LJ_SR, c6= 8.69845432e-03, c12= 2.14014596e-05
40: functype[50]=LJ_SR, c6= 2.81521126e-03, c12= 2.50631820e-06
40: functype[51]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
40: functype[52]=LJ_SR, c6= 2.19084952e-03, c12= 2.43608151e-06
40: functype[53]=LJ_SR, c6= 5.38290978e-04, c12= 2.18128423e-07
40: functype[54]=LJ_SR, c6= 3.39879445e-03, c12= 4.64829665e-06
40: functype[55]=LJ_SR, c6= 2.36385715e-03, c12= 1.58990617e-06
40: functype[56]=LJ_SR, c6= 2.35434729e-03, c12= 2.73168564e-06
40: functype[57]=LJ_SR, c6= 4.88251036e-04, c12= 1.79458653e-07
40: functype[58]=LJ_SR, c6= 5.06604455e-04, c12= 1.49655159e-07
40: functype[59]=LJ_SR, c6= 6.04976375e-03, c12= 7.32016804e-06
40: functype[60]=LJ_SR, c6= 2.80388560e-03, c12= 4.30621225e-06
40: functype[61]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
40: functype[62]=LJ_SR, c6= 2.18203568e-03, c12= 4.18553559e-06
40: functype[63]=LJ_SR, c6= 5.36125420e-04, c12= 3.74775753e-07
40: functype[64]=LJ_SR, c6= 3.38512102e-03, c12= 7.98643684e-06
40: functype[65]=LJ_SR, c6= 2.35434729e-03, c12= 2.73168564e-06
40: functype[66]=LJ_SR, c6= 2.34487570e-03, c12= 4.69342567e-06
40: functype[67]=LJ_SR, c6= 4.86286790e-04, c12= 3.08335570e-07
40: functype[68]=LJ_SR, c6= 5.04566372e-04, c12= 2.57128914e-07
40: functype[69]=LJ_SR, c6= 6.02542540e-03, c12= 1.25770931e-05
40: functype[70]=LJ_SR, c6= 5.81477529e-04, c12= 2.82897505e-07
40: functype[71]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
40: functype[72]=LJ_SR, c6= 4.52516577e-04, c12= 2.74969627e-07
40: functype[73]=LJ_SR, c6= 1.11183168e-04, c12= 2.46209706e-08
40: functype[74]=LJ_SR, c6= 7.02015733e-04, c12= 5.24670621e-07
40: functype[75]=LJ_SR, c6= 4.88251036e-04, c12= 1.79458653e-07
40: functype[76]=LJ_SR, c6= 4.86286790e-04, c12= 3.08335570e-07
40: functype[77]=LJ_SR, c6= 1.00847496e-04, c12= 2.02561691e-08
40: functype[78]=LJ_SR, c6= 1.04638366e-04, c12= 1.68921372e-08
40: functype[79]=LJ_SR, c6= 1.24956934e-03, c12= 8.26254733e-07
40: functype[80]=LJ_SR, c6= 6.03335344e-04, c12= 2.35915461e-07
40: functype[81]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
40: functype[82]=LJ_SR, c6= 4.69526733e-04, c12= 2.29304201e-07
40: functype[83]=LJ_SR, c6= 1.15362558e-04, c12= 2.05320568e-08
40: functype[84]=LJ_SR, c6= 7.28404594e-04, c12= 4.37536244e-07
40: functype[85]=LJ_SR, c6= 5.06604455e-04, c12= 1.49655159e-07
40: functype[86]=LJ_SR, c6= 5.04566372e-04, c12= 2.57128914e-07
40: functype[87]=LJ_SR, c6= 1.04638366e-04, c12= 1.68921372e-08
40: functype[88]=LJ_SR, c6= 1.08571736e-04, c12= 1.40867851e-08
40: functype[89]=LJ_SR, c6= 1.29654081e-03, c12= 6.89034944e-07
40: functype[90]=LJ_SR, c6= 7.20490366e-03, c12= 1.15394674e-05
40: functype[91]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
40: functype[92]=LJ_SR, c6= 5.60698940e-03, c12= 1.12160870e-05
40: functype[93]=LJ_SR, c6= 1.37763538e-03, c12= 1.00429619e-06
40: functype[94]=LJ_SR, c6= 8.69845432e-03, c12= 2.14014596e-05
40: functype[95]=LJ_SR, c6= 6.04976375e-03, c12= 7.32016804e-06
40: functype[96]=LJ_SR, c6= 6.02542540e-03, c12= 1.25770931e-05
40: functype[97]=LJ_SR, c6= 1.24956934e-03, c12= 8.26254733e-07
40: functype[98]=LJ_SR, c6= 1.29654081e-03, c12= 6.89034944e-07
40: functype[99]=LJ_SR, c6= 1.54830174e-02, c12= 3.37031588e-05
40: functype[100]=BONDS, b0A= 1.01000e-01, cbA= 3.63171e+05, b0B= 1.01000e-01, cbB= 3.63171e+05
40: functype[101]=BONDS, b0A= 1.47100e-01, cbA= 3.07106e+05, b0B= 1.47100e-01, cbB= 3.07106e+05
40: functype[102]=BONDS, b0A= 1.09000e-01, cbA= 2.84512e+05, b0B= 1.09000e-01, cbB= 2.84512e+05
40: functype[103]=BONDS, b0A= 1.52900e-01, cbA= 2.24262e+05, b0B= 1.52900e-01, cbB= 2.24262e+05
40: functype[104]=BONDS, b0A= 1.52200e-01, cbA= 2.65266e+05, b0B= 1.52200e-01, cbB= 2.65266e+05
40: functype[105]=BONDS, b0A= 1.22900e-01, cbA= 4.76976e+05, b0B= 1.22900e-01, cbB= 4.76976e+05
40: functype[106]=BONDS, b0A= 1.33500e-01, cbA= 4.10032e+05, b0B= 1.33500e-01, cbB= 4.10032e+05
40: functype[107]=BONDS, b0A= 1.44900e-01, cbA= 2.82002e+05, b0B= 1.44900e-01, cbB= 2.82002e+05
40: functype[108]=BONDS, b0A= 1.51000e-01, cbA= 2.65266e+05, b0B= 1.51000e-01, cbB= 2.65266e+05
40: functype[109]=BONDS, b0A= 1.40000e-01, cbA= 3.92459e+05, b0B= 1.40000e-01, cbB= 3.92459e+05
40: functype[110]=BONDS, b0A= 1.08000e-01, cbA= 3.07106e+05, b0B= 1.08000e-01, cbB= 3.07106e+05
40: functype[111]=BONDS, b0A= 1.46300e-01, cbA= 2.82002e+05, b0B= 1.46300e-01, cbB= 2.82002e+05
40: functype[112]=BONDS, b0A= 1.34000e-01, cbA= 4.02501e+05, b0B= 1.34000e-01, cbB= 4.02501e+05
40: functype[113]=BONDS, b0A= 1.81000e-01, cbA= 1.85770e+05, b0B= 1.81000e-01, cbB= 1.85770e+05
40: functype[114]=BONDS, b0A= 1.33600e-01, cbA= 2.29283e+05, b0B= 1.33600e-01, cbB= 2.29283e+05
40: functype[115]=BONDS, b0A= 1.25000e-01, cbA= 5.48941e+05, b0B= 1.25000e-01, cbB= 5.48941e+05
40: functype[116]=ANGLES, thA= 1.09500e+02, ctA= 2.92880e+02, thB= 1.09500e+02, ctB= 2.92880e+02
40: functype[117]=ANGLES, thA= 1.11200e+02, ctA= 6.69440e+02, thB= 1.11200e+02, ctB= 6.69440e+02
40: functype[118]=ANGLES, thA= 1.10700e+02, ctA= 3.13800e+02, thB= 1.10700e+02, ctB= 3.13800e+02
40: functype[119]=ANGLES, thA= 1.11100e+02, ctA= 5.27184e+02, thB= 1.11100e+02, ctB= 5.27184e+02
40: functype[120]=ANGLES, thA= 1.12700e+02, ctA= 4.88273e+02, thB= 1.12700e+02, ctB= 4.88273e+02
40: functype[121]=ANGLES, thA= 1.07800e+02, ctA= 2.76144e+02, thB= 1.07800e+02, ctB= 2.76144e+02
40: functype[122]=ANGLES, thA= 1.20400e+02, ctA= 6.69440e+02, thB= 1.20400e+02, ctB= 6.69440e+02
40: functype[123]=ANGLES, thA= 1.16600e+02, ctA= 5.85760e+02, thB= 1.16600e+02, ctB= 5.85760e+02
40: functype[124]=ANGLES, thA= 1.22900e+02, ctA= 6.69440e+02, thB= 1.22900e+02, ctB= 6.69440e+02
40: functype[125]=ANGLES, thA= 1.19800e+02, ctA= 2.92880e+02, thB= 1.19800e+02, ctB= 2.92880e+02
40: functype[126]=ANGLES, thA= 1.21900e+02, ctA= 4.18400e+02, thB= 1.21900e+02, ctB= 4.18400e+02
40: functype[127]=ANGLES, thA= 1.18400e+02, ctA= 3.17984e+02, thB= 1.18400e+02, ctB= 3.17984e+02
40: functype[128]=ANGLES, thA= 1.09700e+02, ctA= 6.69440e+02, thB= 1.09700e+02, ctB= 6.69440e+02
40: functype[129]=ANGLES, thA= 1.10100e+02, ctA= 5.27184e+02, thB= 1.10100e+02, ctB= 5.27184e+02
40: functype[130]=ANGLES, thA= 1.14000e+02, ctA= 5.27184e+02, thB= 1.14000e+02, ctB= 5.27184e+02
40: functype[131]=ANGLES, thA= 1.20000e+02, ctA= 5.85760e+02, thB= 1.20000e+02, ctB= 5.85760e+02
40: functype[132]=ANGLES, thA= 1.20000e+02, ctA= 5.27184e+02, thB= 1.20000e+02, ctB= 5.27184e+02
40: functype[133]=ANGLES, thA= 1.20000e+02, ctA= 2.92880e+02, thB= 1.20000e+02, ctB= 2.92880e+02
40: functype[134]=ANGLES, thA= 1.18400e+02, ctA= 2.92880e+02, thB= 1.18400e+02, ctB= 2.92880e+02
40: functype[135]=ANGLES, thA= 1.23200e+02, ctA= 4.18400e+02, thB= 1.23200e+02, ctB= 4.18400e+02
40: functype[136]=ANGLES, thA= 1.08600e+02, ctA= 4.18400e+02, thB= 1.08600e+02, ctB= 4.18400e+02
40: functype[137]=ANGLES, thA= 9.60000e+01, ctA= 3.68192e+02, thB= 9.60000e+01, ctB= 3.68192e+02
40: functype[138]=ANGLES, thA= 1.17000e+02, ctA= 5.85760e+02, thB= 1.17000e+02, ctB= 5.85760e+02
40: functype[139]=ANGLES, thA= 1.26000e+02, ctA= 6.69440e+02, thB= 1.26000e+02, ctB= 6.69440e+02
40: functype[140]=PDIHS, phiA= 1.80000000e+02, cpA= 4.39320000e+01, phiB= 1.80000000e+02, cpB= 4.39320000e+01, mult=2
40: functype[141]=PDIHS, phiA= 1.80000000e+02, cpA= 4.18400000e+00, phiB= 1.80000000e+02, cpB= 4.18400000e+00, mult=2
40: functype[142]=PDIHS, phiA= 1.80000000e+02, cpA= 4.60240000e+00, phiB= 1.80000000e+02, cpB= 4.60240000e+00, mult=2
40: functype[143]=RBDIHS, rbcA[0]= 5.46010000e-01, rbcA[1]= 1.63803000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.18405000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 5.46010000e-01, rbcB[1]= 1.63803000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.18405000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[144]=RBDIHS, rbcA[0]= 7.25920000e-01, rbcA[1]= 2.17777000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.90370000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 7.25920000e-01, rbcB[1]= 2.17777000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.90370000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[145]=RBDIHS, rbcA[0]= 1.27612000e+00, rbcA[1]= 1.16734000e+00, rbcA[2]= 8.95380000e-01, rbcA[3]=-3.33884000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 1.27612000e+00, rbcB[1]= 1.16734000e+00, rbcB[2]= 8.95380000e-01, rbcB[3]=-3.33884000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[146]=RBDIHS, rbcA[0]=-6.91824000e+00, rbcA[1]= 4.67562000e+00, rbcA[2]= 2.24262000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]=-6.91824000e+00, rbcB[1]= 4.67562000e+00, rbcB[2]= 2.24262000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[147]=RBDIHS, rbcA[0]= 9.70690000e-01, rbcA[1]= 2.91206000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.88275000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 9.70690000e-01, rbcB[1]= 2.91206000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.88275000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[148]=RBDIHS, rbcA[0]= 6.27600000e-01, rbcA[1]= 1.88280000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.51040000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 6.27600000e-01, rbcB[1]= 1.88280000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.51040000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[149]=RBDIHS, rbcA[0]=-1.58990000e-01, rbcA[1]=-4.76980000e-01, rbcA[2]= 0.00000000e+00, rbcA[3]= 6.35960000e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]=-1.58990000e-01, rbcB[1]=-4.76980000e-01, rbcB[2]= 0.00000000e+00, rbcB[3]= 6.35960000e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[150]=RBDIHS, rbcA[0]= 1.03637600e+01, rbcA[1]=-6.60654000e+00, rbcA[2]=-1.04934700e+01, rbcA[3]= 6.73624000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 1.03637600e+01, rbcB[1]=-6.60654000e+00, rbcB[2]=-1.04934700e+01, rbcB[3]= 6.73624000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[151]=RBDIHS, rbcA[0]= 5.00825000e+00, rbcA[1]=-1.69870000e+00, rbcA[2]=-3.72380000e-01, rbcA[3]=-2.93716000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 5.00825000e+00, rbcB[1]=-1.69870000e+00, rbcB[2]=-3.72380000e-01, rbcB[3]=-2.93716000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[152]=RBDIHS, rbcA[0]= 2.92880000e+00, rbcA[1]=-1.46440000e+00, rbcA[2]= 2.09200000e-01, rbcA[3]=-1.67360000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 2.92880000e+00, rbcB[1]=-1.46440000e+00, rbcB[2]= 2.09200000e-01, rbcB[3]=-1.67360000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[153]=RBDIHS, rbcA[0]= 5.77183000e+00, rbcA[1]=-2.67148000e+00, rbcA[2]= 9.58140000e-01, rbcA[3]=-4.05848000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 5.77183000e+00, rbcB[1]=-2.67148000e+00, rbcB[2]= 9.58140000e-01, rbcB[3]=-4.05848000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[154]=RBDIHS, rbcA[0]= 8.03330000e-01, rbcA[1]= 2.40999000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.21331000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 8.03330000e-01, rbcB[1]= 2.40999000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.21331000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[155]=RBDIHS, rbcA[0]= 2.05016000e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.05016000e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 2.05016000e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.05016000e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[156]=RBDIHS, rbcA[0]= 3.02879800e+01, rbcA[1]=-4.81160000e+00, rbcA[2]=-2.54763800e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 3.02879800e+01, rbcB[1]=-4.81160000e+00, rbcB[2]=-2.54763800e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[157]=RBDIHS, rbcA[0]= 2.54763800e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.54763800e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 2.54763800e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.54763800e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[158]=RBDIHS, rbcA[0]= 1.57025500e+01, rbcA[1]= 3.17565600e+01, rbcA[2]=-3.66936000e+00, rbcA[3]=-4.37897500e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 1.57025500e+01, rbcB[1]= 3.17565600e+01, rbcB[2]=-3.66936000e+00, rbcB[3]=-4.37897500e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[159]=RBDIHS, rbcA[0]=-1.03574900e+01, rbcA[1]=-2.95871600e+01, rbcA[2]=-1.16734000e+00, rbcA[3]= 4.11119900e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]=-1.03574900e+01, rbcB[1]=-2.95871600e+01, rbcB[2]=-1.16734000e+00, rbcB[3]= 4.11119900e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[160]=RBDIHS, rbcA[0]= 4.50199000e+00, rbcA[1]= 7.82410000e-01, rbcA[2]=-1.60247000e+00, rbcA[3]=-3.68192000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 4.50199000e+00, rbcB[1]= 7.82410000e-01, rbcB[2]=-1.60247000e+00, rbcB[3]=-3.68192000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[161]=RBDIHS, rbcA[0]= 4.22590000e-01, rbcA[1]= 2.70705000e+00, rbcA[2]=-3.12964000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 4.22590000e-01, rbcB[1]= 2.70705000e+00, rbcB[2]=-3.12964000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[162]=RBDIHS, rbcA[0]=-7.65670000e-01, rbcA[1]= 2.70705000e+00, rbcA[2]= 4.02501000e+00, rbcA[3]=-5.96639000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]=-7.65670000e-01, rbcB[1]= 2.70705000e+00, rbcB[2]= 4.02501000e+00, rbcB[3]=-5.96639000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[163]=RBDIHS, rbcA[0]= 9.66500000e-01, rbcA[1]= 2.89951000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.86601000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 9.66500000e-01, rbcB[1]= 2.89951000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.86601000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[164]=RBDIHS, rbcA[0]=-4.23421000e+00, rbcA[1]= 7.22159000e+00, rbcA[2]= 1.90790000e+00, rbcA[3]=-4.89528000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]=-4.23421000e+00, rbcB[1]= 7.22159000e+00, rbcB[2]= 1.90790000e+00, rbcB[3]=-4.89528000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[165]=RBDIHS, rbcA[0]= 3.03340000e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.03340000e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 3.03340000e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.03340000e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[166]=RBDIHS, rbcA[0]= 1.02319700e+01, rbcA[1]= 3.52083000e+00, rbcA[2]=-3.97899000e+00, rbcA[3]=-9.77382000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 1.02319700e+01, rbcB[1]= 3.52083000e+00, rbcB[2]=-3.97899000e+00, rbcB[3]=-9.77382000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[167]=RBDIHS, rbcA[0]= 5.49778000e+00, rbcA[1]= 1.41838000e+00, rbcA[2]=-6.91615000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 5.49778000e+00, rbcB[1]= 1.41838000e+00, rbcB[2]=-6.91615000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[168]=RBDIHS, rbcA[0]=-1.21755000e+00, rbcA[1]=-3.65264000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 4.87018000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]=-1.21755000e+00, rbcB[1]=-3.65264000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 4.87018000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[169]=RBDIHS, rbcA[0]=-1.26775000e+00, rbcA[1]= 3.02085000e+00, rbcA[2]= 1.74473000e+00, rbcA[3]=-3.49782000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]=-1.26775000e+00, rbcB[1]= 3.02085000e+00, rbcB[2]= 1.74473000e+00, rbcB[3]=-3.49782000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[170]=RBDIHS, rbcA[0]= 3.80117000e+00, rbcA[1]=-6.95172000e+00, rbcA[2]=-1.01671000e+00, rbcA[3]= 4.16726000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 3.80117000e+00, rbcB[1]=-6.95172000e+00, rbcB[2]=-1.01671000e+00, rbcB[3]= 4.16726000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[171]=RBDIHS, rbcA[0]= 3.70280000e-01, rbcA[1]= 1.11086000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-1.48114000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 3.70280000e-01, rbcB[1]= 1.11086000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-1.48114000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[172]=RBDIHS, rbcA[0]= 3.32042200e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.32042200e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 3.32042200e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.32042200e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[173]=RBDIHS, rbcA[0]= 1.63176000e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-1.63176000e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 1.63176000e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-1.63176000e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[174]=RBDIHS, rbcA[0]= 3.40787000e+00, rbcA[1]=-2.80537000e+00, rbcA[2]=-3.59820000e-01, rbcA[3]=-2.42670000e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 3.40787000e+00, rbcB[1]=-2.80537000e+00, rbcB[2]=-3.59820000e-01, rbcB[3]=-2.42670000e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[175]=RBDIHS, rbcA[0]=-1.62590200e+01, rbcA[1]= 9.08765000e+00, rbcA[2]= 7.17138000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]=-1.62590200e+01, rbcB[1]= 9.08765000e+00, rbcB[2]= 7.17138000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[176]=RBDIHS, rbcA[0]= 9.45590000e-01, rbcA[1]= 2.83675000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.78234000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 9.45590000e-01, rbcB[1]= 2.83675000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.78234000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[177]=RBDIHS, rbcA[0]=-1.50624000e+00, rbcA[1]= 5.37225000e+00, rbcA[2]= 1.17989000e+00, rbcA[3]=-5.04590000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]=-1.50624000e+00, rbcB[1]= 5.37225000e+00, rbcB[2]= 1.17989000e+00, rbcB[3]=-5.04590000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[178]=RBDIHS, rbcA[0]= 1.00416000e+00, rbcA[1]= 3.01248000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-4.01664000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 1.00416000e+00, rbcB[1]= 3.01248000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-4.01664000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[179]=RBDIHS, rbcA[0]= 8.79268000e+00, rbcA[1]=-1.18344400e+01, rbcA[2]= 1.07529000e+00, rbcA[3]= 1.96648000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 8.79268000e+00, rbcB[1]=-1.18344400e+01, rbcB[2]= 1.07529000e+00, rbcB[3]= 1.96648000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[180]=RBDIHS, rbcA[0]=-5.77392000e+00, rbcA[1]= 3.38485000e+00, rbcA[2]= 2.38906000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]=-5.77392000e+00, rbcB[1]= 3.38485000e+00, rbcB[2]= 2.38906000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[181]=RBDIHS, rbcA[0]=-9.08346000e+00, rbcA[1]= 9.75709000e+00, rbcA[2]= 3.45180000e+00, rbcA[3]=-4.12542000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]=-9.08346000e+00, rbcB[1]= 9.75709000e+00, rbcB[2]= 3.45180000e+00, rbcB[3]=-4.12542000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[182]=RBDIHS, rbcA[0]=-4.70700000e-01, rbcA[1]=-1.41210000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 1.88280000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]=-4.70700000e-01, rbcB[1]=-1.41210000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 1.88280000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[183]=RBDIHS, rbcA[0]= 3.43088000e+00, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.43088000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 3.43088000e+00, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.43088000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[184]=RBDIHS, rbcA[0]= 2.57316000e+00, rbcA[1]= 3.49782000e+00, rbcA[2]=-1.10039000e+00, rbcA[3]=-4.97059000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]= 2.57316000e+00, rbcB[1]= 3.49782000e+00, rbcB[2]=-1.10039000e+00, rbcB[3]=-4.97059000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[185]=RBDIHS, rbcA[0]=-8.22160000e-01, rbcA[1]= 1.12759000e+00, rbcA[2]=-3.05440000e-01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
40: rbcB[0]=-8.22160000e-01, rbcB[1]= 1.12759000e+00, rbcB[2]=-3.05440000e-01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
40: functype[186]=LJ14, c6A= 3.20536041e-04, c12A= 1.71928145e-07, c6B= 3.20536041e-04, c12B= 1.71928145e-07
40: functype[187]=LJ14, c6A= 1.30458481e-03, c12A= 1.92011187e-06, c6B= 1.30458481e-03, c12B= 1.92011187e-06
40: functype[188]=LJ14, c6A= 1.40760563e-03, c12A= 1.25315910e-06, c6B= 1.40760563e-03, c12B= 1.25315910e-06
40: functype[189]=LJ14, c6A= 1.67637339e-03, c12A= 1.97547221e-06, c6B= 1.67637339e-03, c12B= 1.97547221e-06
40: functype[190]=LJ14, c6A= 0.00000000e+00, c12A= 0.00000000e+00, c6B= 0.00000000e+00, c12B= 0.00000000e+00
40: functype[191]=LJ14, c6A= 2.49447081e-04, c12A= 1.67110056e-07, c6B= 2.49447081e-04, c12B= 1.67110056e-07
40: functype[192]=LJ14, c6A= 1.01525205e-03, c12A= 1.86630294e-06, c6B= 1.01525205e-03, c12B= 1.86630294e-06
40: functype[193]=LJ14, c6A= 6.12890625e-05, c12A= 1.49631500e-08, c6B= 6.12890625e-05, c12B= 1.49631500e-08
40: functype[194]=LJ14, c6A= 2.69145489e-04, c12A= 1.09064212e-07, c6B= 2.69145489e-04, c12B= 1.09064212e-07
40: functype[195]=LJ14, c6A= 1.09542476e-03, c12A= 1.21804075e-06, c6B= 1.09542476e-03, c12B= 1.21804075e-06
40: functype[196]=LJ14, c6A= 3.86982011e-04, c12A= 3.18863352e-07, c6B= 3.86982011e-04, c12B= 3.18863352e-07
40: functype[197]=LJ14, c6A= 1.57502055e-03, c12A= 3.56109993e-06, c6B= 1.57502055e-03, c12B= 3.56109993e-06
40: functype[198]=LJ14, c6A= 2.44342255e-03, c12A= 6.79494872e-06, c6B= 2.44342255e-03, c12B= 6.79494872e-06
40: functype[199]=LJ14, c6A= 1.40194280e-03, c12A= 2.15310613e-06, c6B= 1.40194280e-03, c12B= 2.15310613e-06
40: functype[200]=LJ14, c6A= 1.09101784e-03, c12A= 2.09276780e-06, c6B= 1.09101784e-03, c12B= 2.09276780e-06
40: functype[201]=LJ14, c6A= 2.68062710e-04, c12A= 1.87387876e-07, c6B= 2.68062710e-04, c12B= 1.87387876e-07
40: functype[202]=LJ14, c6A= 2.26258289e-04, c12A= 1.37484813e-07, c6B= 2.26258289e-04, c12B= 1.37484813e-07
40: functype[203]=LJ14, c6A= 2.43143395e-04, c12A= 1.54167785e-07, c6B= 2.43143395e-04, c12B= 1.54167785e-07
40: functype[204]=LJ14, c6A= 1.17243785e-03, c12A= 2.34671283e-06, c6B= 1.17243785e-03, c12B= 2.34671283e-06
40: functype[205]=LJ14, c6A= 1.69256051e-03, c12A= 3.99321842e-06, c6B= 1.69256051e-03, c12B= 3.99321842e-06
40: functype[206]=LJ14, c6A= 5.04237478e-05, c12A= 1.01280845e-08, c6B= 5.04237478e-05, c12B= 1.01280845e-08
40: functype[207]=LJ14, c6A= 2.34763367e-04, c12A= 1.14652101e-07, c6B= 2.34763367e-04, c12B= 1.14652101e-07
40: functype[208]=LJ14, c6A= 5.76812790e-05, c12A= 1.02660284e-08, c6B= 5.76812790e-05, c12B= 1.02660284e-08
40: functype[209]=LJ14, c6A= 3.60245183e-03, c12A= 5.76973368e-06, c6B= 3.60245183e-03, c12B= 5.76973368e-06
40: functype[210]=LJ14, c6A= 6.88817690e-04, c12A= 5.02148096e-07, c6B= 6.88817690e-04, c12B= 5.02148096e-07
40: functype[211]=LJ14, c6A= 4.34922716e-03, c12A= 1.07007298e-05, c6B= 4.34922716e-03, c12B= 1.07007298e-05
40: reppow = 12
40: fudgeQQ = 0.5
40: cmap
40: atomtypes:
40: atomtype[ 0]={atomnumber= 7}
40: atomtype[ 1]={atomnumber= 1}
40: atomtype[ 2]={atomnumber= 6}
40: atomtype[ 3]={atomnumber= 1}
40: atomtype[ 4]={atomnumber= 6}
40: atomtype[ 5]={atomnumber= 8}
40: atomtype[ 6]={atomnumber= 6}
40: atomtype[ 7]={atomnumber= 1}
40: atomtype[ 8]={atomnumber= 6}
40: atomtype[ 9]={atomnumber= 16}
40: moltype (0):
40: name="Protein_chain_B"
40: atoms:
40: atom (156):
40: atom[ 0]={type= 0, typeB= 0, ptype= Atom, m= 1.40027e+01, q=-3.00000e-01, mB= 1.40027e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7}
40: atom[ 1]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
40: atom[ 2]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
40: atom[ 3]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
40: atom[ 4]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 2.50000e-01, mB= 1.20110e+01, qB= 2.50000e-01, resind= 0, atomnumber= 6}
40: atom[ 5]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
40: atom[ 6]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6}
40: atom[ 7]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
40: atom[ 8]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
40: atom[ 9]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6}
40: atom[ 10]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
40: atom[ 11]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
40: atom[ 12]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6}
40: atom[ 13]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
40: atom[ 14]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
40: atom[ 15]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 0, atomnumber= 6}
40: atom[ 16]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
40: atom[ 17]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
40: atom[ 18]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-3.00000e-01, mB= 1.40067e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7}
40: atom[ 19]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
40: atom[ 20]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
40: atom[ 21]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
40: atom[ 22]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 0, atomnumber= 6}
40: atom[ 23]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 0, atomnumber= 8}
40: atom[ 24]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 1, atomnumber= 7}
40: atom[ 25]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 1, atomnumber= 1}
40: atom[ 26]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 1, atomnumber= 6}
40: atom[ 27]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
40: atom[ 28]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 1, atomnumber= 6}
40: atom[ 29]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
40: atom[ 30]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6}
40: atom[ 31]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
40: atom[ 32]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
40: atom[ 33]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
40: atom[ 34]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6}
40: atom[ 35]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
40: atom[ 36]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
40: atom[ 37]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
40: atom[ 38]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 1, atomnumber= 6}
40: atom[ 39]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 1, atomnumber= 8}
40: atom[ 40]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 2, atomnumber= 7}
40: atom[ 41]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 2, atomnumber= 1}
40: atom[ 42]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 2, atomnumber= 6}
40: atom[ 43]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1}
40: atom[ 44]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-03, mB= 1.20110e+01, qB=-5.00000e-03, resind= 2, atomnumber= 6}
40: atom[ 45]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1}
40: atom[ 46]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1}
40: atom[ 47]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
40: atom[ 48]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
40: atom[ 49]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1}
40: atom[ 50]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
40: atom[ 51]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1}
40: atom[ 52]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
40: atom[ 53]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1}
40: atom[ 54]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
40: atom[ 55]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1}
40: atom[ 56]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
40: atom[ 57]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1}
40: atom[ 58]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 2, atomnumber= 6}
40: atom[ 59]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 2, atomnumber= 8}
40: atom[ 60]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 3, atomnumber= 7}
40: atom[ 61]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 3, atomnumber= 1}
40: atom[ 62]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 8.00000e-02, mB= 1.20110e+01, qB= 8.00000e-02, resind= 3, atomnumber= 6}
40: atom[ 63]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1}
40: atom[ 64]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1}
40: atom[ 65]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 3, atomnumber= 6}
40: atom[ 66]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 3, atomnumber= 8}
40: atom[ 67]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 4, atomnumber= 7}
40: atom[ 68]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 4, atomnumber= 1}
40: atom[ 69]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 4, atomnumber= 6}
40: atom[ 70]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
40: atom[ 71]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 4, atomnumber= 6}
40: atom[ 72]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
40: atom[ 73]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
40: atom[ 74]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-02, mB= 1.20110e+01, qB=-5.00000e-02, resind= 4, atomnumber= 6}
40: atom[ 75]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
40: atom[ 76]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
40: atom[ 77]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 4, atomnumber= 6}
40: atom[ 78]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
40: atom[ 79]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
40: atom[ 80]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-7.00000e-01, mB= 1.40067e+01, qB=-7.00000e-01, resind= 4, atomnumber= 7}
40: atom[ 81]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.40000e-01, mB= 1.00800e+00, qB= 4.40000e-01, resind= 4, atomnumber= 1}
40: atom[ 82]={type= 8, typeB= 8, ptype= Atom, m= 1.20110e+01, q= 6.40000e-01, mB= 1.20110e+01, qB= 6.40000e-01, resind= 4, atomnumber= 6}
40: atom[ 83]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7}
40: atom[ 84]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1}
40: atom[ 85]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1}
40: atom[ 86]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7}
40: atom[ 87]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1}
40: atom[ 88]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1}
40: atom[ 89]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 4, atomnumber= 6}
40: atom[ 90]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 4, atomnumber= 8}
40: atom[ 91]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 5, atomnumber= 7}
40: atom[ 92]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 5, atomnumber= 1}
40: atom[ 93]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 5, atomnumber= 6}
40: atom[ 94]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1}
40: atom[ 95]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 6.00000e-02, mB= 1.20110e+01, qB= 6.00000e-02, resind= 5, atomnumber= 6}
40: atom[ 96]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1}
40: atom[ 97]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1}
40: atom[ 98]={type= 9, typeB= 9, ptype= Atom, m= 3.20600e+01, q=-3.35000e-01, mB= 3.20600e+01, qB=-3.35000e-01, resind= 5, atomnumber= 16}
40: atom[ 99]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 1.55000e-01, mB= 1.00800e+00, qB= 1.55000e-01, resind= 5, atomnumber= 1}
40: atom[ 100]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 5, atomnumber= 6}
40: atom[ 101]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 5, atomnumber= 8}
40: atom[ 102]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 6, atomnumber= 7}
40: atom[ 103]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 6, atomnumber= 1}
40: atom[ 104]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 6, atomnumber= 6}
40: atom[ 105]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1}
40: atom[ 106]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 6, atomnumber= 6}
40: atom[ 107]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1}
40: atom[ 108]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1}
40: atom[ 109]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-2.20000e-01, mB= 1.20110e+01, qB=-2.20000e-01, resind= 6, atomnumber= 6}
40: atom[ 110]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1}
40: atom[ 111]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1}
40: atom[ 112]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 7.00000e-01, mB= 1.20110e+01, qB= 7.00000e-01, resind= 6, atomnumber= 6}
40: atom[ 113]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8}
40: atom[ 114]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8}
40: atom[ 115]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 6, atomnumber= 6}
40: atom[ 116]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 6, atomnumber= 8}
40: atom[ 117]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 7, atomnumber= 7}
40: atom[ 118]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 7, atomnumber= 1}
40: atom[ 119]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 7, atomnumber= 6}
40: atom[ 120]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
40: atom[ 121]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 7, atomnumber= 6}
40: atom[ 122]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
40: atom[ 123]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
40: atom[ 124]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 7, atomnumber= 6}
40: atom[ 125]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
40: atom[ 126]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6}
40: atom[ 127]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
40: atom[ 128]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
40: atom[ 129]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
40: atom[ 130]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6}
40: atom[ 131]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
40: atom[ 132]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
40: atom[ 133]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
40: atom[ 134]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 7, atomnumber= 6}
40: atom[ 135]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 7, atomnumber= 8}
40: atom[ 136]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 8, atomnumber= 7}
40: atom[ 137]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 8, atomnumber= 1}
40: atom[ 138]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 8, atomnumber= 6}
40: atom[ 139]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1}
40: atom[ 140]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 8, atomnumber= 6}
40: atom[ 141]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1}
40: atom[ 142]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1}
40: atom[ 143]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1}
40: atom[ 144]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 8, atomnumber= 6}
40: atom[ 145]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 8, atomnumber= 8}
40: atom[ 146]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 9, atomnumber= 7}
40: atom[ 147]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 9, atomnumber= 1}
40: atom[ 148]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 9, atomnumber= 6}
40: atom[ 149]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1}
40: atom[ 150]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 9, atomnumber= 6}
40: atom[ 151]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1}
40: atom[ 152]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1}
40: atom[ 153]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1}
40: atom[ 154]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 9, atomnumber= 6}
40: atom[ 155]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 9, atomnumber= 8}
40: atom (156):
40: atom[0]={name="N"}
40: atom[1]={name="H1"}
40: atom[2]={name="H2"}
40: atom[3]={name="H3"}
40: atom[4]={name="CA"}
40: atom[5]={name="HA"}
40: atom[6]={name="CB"}
40: atom[7]={name="HB1"}
40: atom[8]={name="HB2"}
40: atom[9]={name="CG"}
40: atom[10]={name="HG1"}
40: atom[11]={name="HG2"}
40: atom[12]={name="CD"}
40: atom[13]={name="HD1"}
40: atom[14]={name="HD2"}
40: atom[15]={name="CE"}
40: atom[16]={name="HE1"}
40: atom[17]={name="HE2"}
40: atom[18]={name="NZ"}
40: atom[19]={name="HZ1"}
40: atom[20]={name="HZ2"}
40: atom[21]={name="HZ3"}
40: atom[22]={name="C"}
40: atom[23]={name="O"}
40: atom[24]={name="N"}
40: atom[25]={name="H"}
40: atom[26]={name="CA"}
40: atom[27]={name="HA"}
40: atom[28]={name="CB"}
40: atom[29]={name="HB"}
40: atom[30]={name="CG1"}
40: atom[31]={name="HG11"}
40: atom[32]={name="HG12"}
40: atom[33]={name="HG13"}
40: atom[34]={name="CG2"}
40: atom[35]={name="HG21"}
40: atom[36]={name="HG22"}
40: atom[37]={name="HG23"}
40: atom[38]={name="C"}
40: atom[39]={name="O"}
40: atom[40]={name="N"}
40: atom[41]={name="H"}
40: atom[42]={name="CA"}
40: atom[43]={name="HA"}
40: atom[44]={name="CB"}
40: atom[45]={name="HB1"}
40: atom[46]={name="HB2"}
40: atom[47]={name="CG"}
40: atom[48]={name="CD1"}
40: atom[49]={name="HD1"}
40: atom[50]={name="CD2"}
40: atom[51]={name="HD2"}
40: atom[52]={name="CE1"}
40: atom[53]={name="HE1"}
40: atom[54]={name="CE2"}
40: atom[55]={name="HE2"}
40: atom[56]={name="CZ"}
40: atom[57]={name="HZ"}
40: atom[58]={name="C"}
40: atom[59]={name="O"}
40: atom[60]={name="N"}
40: atom[61]={name="H"}
40: atom[62]={name="CA"}
40: atom[63]={name="HA1"}
40: atom[64]={name="HA2"}
40: atom[65]={name="C"}
40: atom[66]={name="O"}
40: atom[67]={name="N"}
40: atom[68]={name="H"}
40: atom[69]={name="CA"}
40: atom[70]={name="HA"}
40: atom[71]={name="CB"}
40: atom[72]={name="HB1"}
40: atom[73]={name="HB2"}
40: atom[74]={name="CG"}
40: atom[75]={name="HG1"}
40: atom[76]={name="HG2"}
40: atom[77]={name="CD"}
40: atom[78]={name="HD1"}
40: atom[79]={name="HD2"}
40: atom[80]={name="NE"}
40: atom[81]={name="HE"}
40: atom[82]={name="CZ"}
40: atom[83]={name="NH1"}
40: atom[84]={name="HH11"}
40: atom[85]={name="HH12"}
40: atom[86]={name="NH2"}
40: atom[87]={name="HH21"}
40: atom[88]={name="HH22"}
40: atom[89]={name="C"}
40: atom[90]={name="O"}
40: atom[91]={name="N"}
40: atom[92]={name="H"}
40: atom[93]={name="CA"}
40: atom[94]={name="HA"}
40: atom[95]={name="CB"}
40: atom[96]={name="HB1"}
40: atom[97]={name="HB2"}
40: atom[98]={name="SG"}
40: atom[99]={name="HG"}
40: atom[100]={name="C"}
40: atom[101]={name="O"}
40: atom[102]={name="N"}
40: atom[103]={name="H"}
40: atom[104]={name="CA"}
40: atom[105]={name="HA"}
40: atom[106]={name="CB"}
40: atom[107]={name="HB1"}
40: atom[108]={name="HB2"}
40: atom[109]={name="CG"}
40: atom[110]={name="HG1"}
40: atom[111]={name="HG2"}
40: atom[112]={name="CD"}
40: atom[113]={name="OE1"}
40: atom[114]={name="OE2"}
40: atom[115]={name="C"}
40: atom[116]={name="O"}
40: atom[117]={name="N"}
40: atom[118]={name="H"}
40: atom[119]={name="CA"}
40: atom[120]={name="HA"}
40: atom[121]={name="CB"}
40: atom[122]={name="HB1"}
40: atom[123]={name="HB2"}
40: atom[124]={name="CG"}
40: atom[125]={name="HG"}
40: atom[126]={name="CD1"}
40: atom[127]={name="HD11"}
40: atom[128]={name="HD12"}
40: atom[129]={name="HD13"}
40: atom[130]={name="CD2"}
40: atom[131]={name="HD21"}
40: atom[132]={name="HD22"}
40: atom[133]={name="HD23"}
40: atom[134]={name="C"}
40: atom[135]={name="O"}
40: atom[136]={name="N"}
40: atom[137]={name="H"}
40: atom[138]={name="CA"}
40: atom[139]={name="HA"}
40: atom[140]={name="CB"}
40: atom[141]={name="HB1"}
40: atom[142]={name="HB2"}
40: atom[143]={name="HB3"}
40: atom[144]={name="C"}
40: atom[145]={name="O"}
40: atom[146]={name="N"}
40: atom[147]={name="H"}
40: atom[148]={name="CA"}
40: atom[149]={name="HA"}
40: atom[150]={name="CB"}
40: atom[151]={name="HB1"}
40: atom[152]={name="HB2"}
40: atom[153]={name="HB3"}
40: atom[154]={name="C"}
40: atom[155]={name="O"}
40: type (156):
40: type[0]={name="opls_287",nameB="opls_287"}
40: type[1]={name="opls_290",nameB="opls_290"}
40: type[2]={name="opls_290",nameB="opls_290"}
40: type[3]={name="opls_290",nameB="opls_290"}
40: type[4]={name="opls_293B",nameB="opls_293B"}
40: type[5]={name="opls_140",nameB="opls_140"}
40: type[6]={name="opls_136",nameB="opls_136"}
40: type[7]={name="opls_140",nameB="opls_140"}
40: type[8]={name="opls_140",nameB="opls_140"}
40: type[9]={name="opls_136",nameB="opls_136"}
40: type[10]={name="opls_140",nameB="opls_140"}
40: type[11]={name="opls_140",nameB="opls_140"}
40: type[12]={name="opls_136",nameB="opls_136"}
40: type[13]={name="opls_140",nameB="opls_140"}
40: type[14]={name="opls_140",nameB="opls_140"}
40: type[15]={name="opls_292",nameB="opls_292"}
40: type[16]={name="opls_140",nameB="opls_140"}
40: type[17]={name="opls_140",nameB="opls_140"}
40: type[18]={name="opls_287",nameB="opls_287"}
40: type[19]={name="opls_290",nameB="opls_290"}
40: type[20]={name="opls_290",nameB="opls_290"}
40: type[21]={name="opls_290",nameB="opls_290"}
40: type[22]={name="opls_235",nameB="opls_235"}
40: type[23]={name="opls_236",nameB="opls_236"}
40: type[24]={name="opls_238",nameB="opls_238"}
40: type[25]={name="opls_241",nameB="opls_241"}
40: type[26]={name="opls_224B",nameB="opls_224B"}
40: type[27]={name="opls_140",nameB="opls_140"}
40: type[28]={name="opls_137",nameB="opls_137"}
40: type[29]={name="opls_140",nameB="opls_140"}
40: type[30]={name="opls_135",nameB="opls_135"}
40: type[31]={name="opls_140",nameB="opls_140"}
40: type[32]={name="opls_140",nameB="opls_140"}
40: type[33]={name="opls_140",nameB="opls_140"}
40: type[34]={name="opls_135",nameB="opls_135"}
40: type[35]={name="opls_140",nameB="opls_140"}
40: type[36]={name="opls_140",nameB="opls_140"}
40: type[37]={name="opls_140",nameB="opls_140"}
40: type[38]={name="opls_235",nameB="opls_235"}
40: type[39]={name="opls_236",nameB="opls_236"}
40: type[40]={name="opls_238",nameB="opls_238"}
40: type[41]={name="opls_241",nameB="opls_241"}
40: type[42]={name="opls_224B",nameB="opls_224B"}
40: type[43]={name="opls_140",nameB="opls_140"}
40: type[44]={name="opls_149",nameB="opls_149"}
40: type[45]={name="opls_140",nameB="opls_140"}
40: type[46]={name="opls_140",nameB="opls_140"}
40: type[47]={name="opls_145",nameB="opls_145"}
40: type[48]={name="opls_145",nameB="opls_145"}
40: type[49]={name="opls_146",nameB="opls_146"}
40: type[50]={name="opls_145",nameB="opls_145"}
40: type[51]={name="opls_146",nameB="opls_146"}
40: type[52]={name="opls_145",nameB="opls_145"}
40: type[53]={name="opls_146",nameB="opls_146"}
40: type[54]={name="opls_145",nameB="opls_145"}
40: type[55]={name="opls_146",nameB="opls_146"}
40: type[56]={name="opls_145",nameB="opls_145"}
40: type[57]={name="opls_146",nameB="opls_146"}
40: type[58]={name="opls_235",nameB="opls_235"}
40: type[59]={name="opls_236",nameB="opls_236"}
40: type[60]={name="opls_238",nameB="opls_238"}
40: type[61]={name="opls_241",nameB="opls_241"}
40: type[62]={name="opls_223B",nameB="opls_223B"}
40: type[63]={name="opls_140",nameB="opls_140"}
40: type[64]={name="opls_140",nameB="opls_140"}
40: type[65]={name="opls_235",nameB="opls_235"}
40: type[66]={name="opls_236",nameB="opls_236"}
40: type[67]={name="opls_238",nameB="opls_238"}
40: type[68]={name="opls_241",nameB="opls_241"}
40: type[69]={name="opls_224B",nameB="opls_224B"}
40: type[70]={name="opls_140",nameB="opls_140"}
40: type[71]={name="opls_136",nameB="opls_136"}
40: type[72]={name="opls_140",nameB="opls_140"}
40: type[73]={name="opls_140",nameB="opls_140"}
40: type[74]={name="opls_308",nameB="opls_308"}
40: type[75]={name="opls_140",nameB="opls_140"}
40: type[76]={name="opls_140",nameB="opls_140"}
40: type[77]={name="opls_307",nameB="opls_307"}
40: type[78]={name="opls_140",nameB="opls_140"}
40: type[79]={name="opls_140",nameB="opls_140"}
40: type[80]={name="opls_303",nameB="opls_303"}
40: type[81]={name="opls_304",nameB="opls_304"}
40: type[82]={name="opls_302",nameB="opls_302"}
40: type[83]={name="opls_300",nameB="opls_300"}
40: type[84]={name="opls_301",nameB="opls_301"}
40: type[85]={name="opls_301",nameB="opls_301"}
40: type[86]={name="opls_300",nameB="opls_300"}
40: type[87]={name="opls_301",nameB="opls_301"}
40: type[88]={name="opls_301",nameB="opls_301"}
40: type[89]={name="opls_235",nameB="opls_235"}
40: type[90]={name="opls_236",nameB="opls_236"}
40: type[91]={name="opls_238",nameB="opls_238"}
40: type[92]={name="opls_241",nameB="opls_241"}
40: type[93]={name="opls_224B",nameB="opls_224B"}
40: type[94]={name="opls_140",nameB="opls_140"}
40: type[95]={name="opls_206",nameB="opls_206"}
40: type[96]={name="opls_140",nameB="opls_140"}
40: type[97]={name="opls_140",nameB="opls_140"}
40: type[98]={name="opls_200",nameB="opls_200"}
40: type[99]={name="opls_204",nameB="opls_204"}
40: type[100]={name="opls_235",nameB="opls_235"}
40: type[101]={name="opls_236",nameB="opls_236"}
40: type[102]={name="opls_238",nameB="opls_238"}
40: type[103]={name="opls_241",nameB="opls_241"}
40: type[104]={name="opls_224B",nameB="opls_224B"}
40: type[105]={name="opls_140",nameB="opls_140"}
40: type[106]={name="opls_136",nameB="opls_136"}
40: type[107]={name="opls_140",nameB="opls_140"}
40: type[108]={name="opls_140",nameB="opls_140"}
40: type[109]={name="opls_274",nameB="opls_274"}
40: type[110]={name="opls_140",nameB="opls_140"}
40: type[111]={name="opls_140",nameB="opls_140"}
40: type[112]={name="opls_271",nameB="opls_271"}
40: type[113]={name="opls_272",nameB="opls_272"}
40: type[114]={name="opls_272",nameB="opls_272"}
40: type[115]={name="opls_235",nameB="opls_235"}
40: type[116]={name="opls_236",nameB="opls_236"}
40: type[117]={name="opls_238",nameB="opls_238"}
40: type[118]={name="opls_241",nameB="opls_241"}
40: type[119]={name="opls_224B",nameB="opls_224B"}
40: type[120]={name="opls_140",nameB="opls_140"}
40: type[121]={name="opls_136",nameB="opls_136"}
40: type[122]={name="opls_140",nameB="opls_140"}
40: type[123]={name="opls_140",nameB="opls_140"}
40: type[124]={name="opls_137",nameB="opls_137"}
40: type[125]={name="opls_140",nameB="opls_140"}
40: type[126]={name="opls_135",nameB="opls_135"}
40: type[127]={name="opls_140",nameB="opls_140"}
40: type[128]={name="opls_140",nameB="opls_140"}
40: type[129]={name="opls_140",nameB="opls_140"}
40: type[130]={name="opls_135",nameB="opls_135"}
40: type[131]={name="opls_140",nameB="opls_140"}
40: type[132]={name="opls_140",nameB="opls_140"}
40: type[133]={name="opls_140",nameB="opls_140"}
40: type[134]={name="opls_235",nameB="opls_235"}
40: type[135]={name="opls_236",nameB="opls_236"}
40: type[136]={name="opls_238",nameB="opls_238"}
40: type[137]={name="opls_241",nameB="opls_241"}
40: type[138]={name="opls_224B",nameB="opls_224B"}
40: type[139]={name="opls_140",nameB="opls_140"}
40: type[140]={name="opls_135",nameB="opls_135"}
40: type[141]={name="opls_140",nameB="opls_140"}
40: type[142]={name="opls_140",nameB="opls_140"}
40: type[143]={name="opls_140",nameB="opls_140"}
40: type[144]={name="opls_235",nameB="opls_235"}
40: type[145]={name="opls_236",nameB="opls_236"}
40: type[146]={name="opls_238",nameB="opls_238"}
40: type[147]={name="opls_241",nameB="opls_241"}
40: type[148]={name="opls_224B",nameB="opls_224B"}
40: type[149]={name="opls_140",nameB="opls_140"}
40: type[150]={name="opls_135",nameB="opls_135"}
40: type[151]={name="opls_140",nameB="opls_140"}
40: type[152]={name="opls_140",nameB="opls_140"}
40: type[153]={name="opls_140",nameB="opls_140"}
40: type[154]={name="opls_235",nameB="opls_235"}
40: type[155]={name="opls_236",nameB="opls_236"}
40: residue (10):
40: residue[0]={name="LYS", nr=1, ic=' '}
40: residue[1]={name="VAL", nr=2, ic=' '}
40: residue[2]={name="PHE", nr=3, ic=' '}
40: residue[3]={name="GLY", nr=4, ic=' '}
40: residue[4]={name="ARG", nr=5, ic=' '}
40: residue[5]={name="CYS", nr=6, ic=' '}
40: residue[6]={name="GLU", nr=7, ic=' '}
40: residue[7]={name="LEU", nr=8, ic=' '}
40: residue[8]={name="ALA", nr=9, ic=' '}
40: residue[9]={name="ALA", nr=10, ic=' '}
40: excls:
40: nr=156
40: nra=1828
40: excls[0][0..12]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24}
40: excls[1][13..20]={0, 1, 2, 3, 4, 5, 6, 22}
40: excls[2][21..28]={0, 1, 2, 3, 4, 5, 6, 22}
40: excls[3][29..36]={0, 1, 2, 3, 4, 5, 6, 22}
40: excls[4][37..54]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22,
40: 23, 24, 25, 26}
40: excls[5][55..67]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24}
40: excls[6][68..86]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13,
40: 14, 15, 22, 23, 24}
40: excls[7][87..97]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22}
40: excls[8][98..108]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22}
40: excls[9][109..125]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,
40: 16, 17, 18, 22}
40: excls[10][126..136]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15}
40: excls[11][137..147]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15}
40: excls[12][148..164]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16,
40: 17, 18, 19, 20, 21}
40: excls[13][165..175]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18}
40: excls[14][176..186]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18}
40: excls[15][187..200]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18,
40: 19, 20, 21}
40: excls[16][201..211]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21}
40: excls[17][212..222]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21}
40: excls[18][223..233]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21}
40: excls[19][234..241]={12, 15, 16, 17, 18, 19, 20, 21}
40: excls[20][242..249]={12, 15, 16, 17, 18, 19, 20, 21}
40: excls[21][250..257]={12, 15, 16, 17, 18, 19, 20, 21}
40: excls[22][258..275]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24,
40: 25, 26, 27, 28, 38}
40: excls[23][276..284]={0, 4, 5, 6, 22, 23, 24, 25, 26}
40: excls[24][285..301]={0, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29,
40: 30, 34, 38, 39, 40}
40: excls[25][302..310]={4, 22, 23, 24, 25, 26, 27, 28, 38}
40: excls[26][311..332]={4, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31,
40: 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42}
40: excls[27][333..344]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39,
40: 40}
40: excls[28][345..362]={22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33,
40: 34, 35, 36, 37, 38, 39, 40}
40: excls[29][363..376]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,
40: 36, 37, 38}
40: excls[30][377..390]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,
40: 36, 37, 38}
40: excls[31][391..398]={26, 28, 29, 30, 31, 32, 33, 34}
40: excls[32][399..406]={26, 28, 29, 30, 31, 32, 33, 34}
40: excls[33][407..414]={26, 28, 29, 30, 31, 32, 33, 34}
40: excls[34][415..428]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,
40: 36, 37, 38}
40: excls[35][429..436]={26, 28, 29, 30, 34, 35, 36, 37}
40: excls[36][437..444]={26, 28, 29, 30, 34, 35, 36, 37}
40: excls[37][445..452]={26, 28, 29, 30, 34, 35, 36, 37}
40: excls[38][453..469]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39,
40: 40, 41, 42, 43, 44, 58}
40: excls[39][470..478]={24, 26, 27, 28, 38, 39, 40, 41, 42}
40: excls[40][479..495]={24, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44,
40: 45, 46, 47, 58, 59, 60}
40: excls[41][496..504]={26, 38, 39, 40, 41, 42, 43, 44, 58}
40: excls[42][505..522]={26, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47,
40: 48, 50, 58, 59, 60, 61, 62}
40: excls[43][523..534]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59,
40: 60}
40: excls[44][535..552]={38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49,
40: 50, 51, 52, 54, 58, 59, 60}
40: excls[45][553..562]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58}
40: excls[46][563..572]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58}
40: excls[47][573..589]={40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51,
40: 52, 53, 54, 55, 56, 58}
40: excls[48][590..603]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53,
40: 54, 56, 57}
40: excls[49][604..611]={44, 47, 48, 49, 50, 52, 53, 56}
40: excls[50][612..625]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54,
40: 55, 56, 57}
40: excls[51][626..633]={44, 47, 48, 50, 51, 54, 55, 56}
40: excls[52][634..644]={44, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57}
40: excls[53][645..652]={47, 48, 49, 52, 53, 54, 56, 57}
40: excls[54][653..663]={44, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57}
40: excls[55][664..671]={47, 50, 51, 52, 54, 55, 56, 57}
40: excls[56][672..682]={47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57}
40: excls[57][683..690]={48, 50, 52, 53, 54, 55, 56, 57}
40: excls[58][691..707]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59,
40: 60, 61, 62, 63, 64, 65}
40: excls[59][708..716]={40, 42, 43, 44, 58, 59, 60, 61, 62}
40: excls[60][717..730]={40, 42, 43, 44, 58, 59, 60, 61, 62, 63, 64,
40: 65, 66, 67}
40: excls[61][731..739]={42, 58, 59, 60, 61, 62, 63, 64, 65}
40: excls[62][740..752]={42, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67,
40: 68, 69}
40: excls[63][753..761]={58, 60, 61, 62, 63, 64, 65, 66, 67}
40: excls[64][762..770]={58, 60, 61, 62, 63, 64, 65, 66, 67}
40: excls[65][771..784]={58, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69,
40: 70, 71, 89}
40: excls[66][785..793]={60, 62, 63, 64, 65, 66, 67, 68, 69}
40: excls[67][794..810]={60, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71,
40: 72, 73, 74, 89, 90, 91}
40: excls[68][811..819]={62, 65, 66, 67, 68, 69, 70, 71, 89}
40: excls[69][820..838]={62, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74,
40: 75, 76, 77, 89, 90, 91, 92, 93}
40: excls[70][839..850]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90,
40: 91}
40: excls[71][851..868]={65, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76,
40: 77, 78, 79, 80, 89, 90, 91}
40: excls[72][869..879]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89}
40: excls[73][880..890]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89}
40: excls[74][891..906]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78,
40: 79, 80, 81, 82, 89}
40: excls[75][907..917]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80}
40: excls[76][918..928]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80}
40: excls[77][929..943]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80,
40: 81, 82, 83, 86}
40: excls[78][944..953]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82}
40: excls[79][954..963]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82}
40: excls[80][964..979]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83,
40: 84, 85, 86, 87, 88}
40: excls[81][980..988]={74, 77, 78, 79, 80, 81, 82, 83, 86}
40: excls[82][989..1001]={74, 77, 78, 79, 80, 81, 82, 83, 84, 85,
40: 86, 87, 88}
40: excls[83][1002..1011]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88}
40: excls[84][1012..1017]={80, 82, 83, 84, 85, 86}
40: excls[85][1018..1023]={80, 82, 83, 84, 85, 86}
40: excls[86][1024..1033]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88}
40: excls[87][1034..1039]={80, 82, 83, 86, 87, 88}
40: excls[88][1040..1045]={80, 82, 83, 86, 87, 88}
40: excls[89][1046..1062]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89,
40: 90, 91, 92, 93, 94, 95, 100}
40: excls[90][1063..1071]={67, 69, 70, 71, 89, 90, 91, 92, 93}
40: excls[91][1072..1088]={67, 69, 70, 71, 89, 90, 91, 92, 93, 94,
40: 95, 96, 97, 98, 100, 101, 102}
40: excls[92][1089..1097]={69, 89, 90, 91, 92, 93, 94, 95, 100}
40: excls[93][1098..1114]={69, 89, 90, 91, 92, 93, 94, 95, 96, 97,
40: 98, 99, 100, 101, 102, 103, 104}
40: excls[94][1115..1126]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100,
40: 101, 102}
40: excls[95][1127..1139]={89, 91, 92, 93, 94, 95, 96, 97, 98, 99,
40: 100, 101, 102}
40: excls[96][1140..1148]={91, 93, 94, 95, 96, 97, 98, 99, 100}
40: excls[97][1149..1157]={91, 93, 94, 95, 96, 97, 98, 99, 100}
40: excls[98][1158..1166]={91, 93, 94, 95, 96, 97, 98, 99, 100}
40: excls[99][1167..1172]={93, 95, 96, 97, 98, 99}
40: excls[100][1173..1189]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100,
40: 101, 102, 103, 104, 105, 106, 115}
40: excls[101][1190..1198]={91, 93, 94, 95, 100, 101, 102, 103, 104}
40: excls[102][1199..1215]={91, 93, 94, 95, 100, 101, 102, 103, 104,
40: 105, 106, 107, 108, 109, 115, 116, 117}
40: excls[103][1216..1224]={93, 100, 101, 102, 103, 104, 105, 106,
40: 115}
40: excls[104][1225..1243]={93, 100, 101, 102, 103, 104, 105, 106,
40: 107, 108, 109, 110, 111, 112, 115, 116, 117, 118, 119}
40: excls[105][1244..1255]={100, 102, 103, 104, 105, 106, 107, 108,
40: 109, 115, 116, 117}
40: excls[106][1256..1272]={100, 102, 103, 104, 105, 106, 107, 108,
40: 109, 110, 111, 112, 113, 114, 115, 116, 117}
40: excls[107][1273..1283]={102, 104, 105, 106, 107, 108, 109, 110,
40: 111, 112, 115}
40: excls[108][1284..1294]={102, 104, 105, 106, 107, 108, 109, 110,
40: 111, 112, 115}
40: excls[109][1295..1307]={102, 104, 105, 106, 107, 108, 109, 110,
40: 111, 112, 113, 114, 115}
40: excls[110][1308..1317]={104, 106, 107, 108, 109, 110, 111, 112,
40: 113, 114}
40: excls[111][1318..1327]={104, 106, 107, 108, 109, 110, 111, 112,
40: 113, 114}
40: excls[112][1328..1337]={104, 106, 107, 108, 109, 110, 111, 112,
40: 113, 114}
40: excls[113][1338..1344]={106, 109, 110, 111, 112, 113, 114}
40: excls[114][1345..1351]={106, 109, 110, 111, 112, 113, 114}
40: excls[115][1352..1368]={100, 102, 103, 104, 105, 106, 107, 108,
40: 109, 115, 116, 117, 118, 119, 120, 121, 134}
40: excls[116][1369..1377]={102, 104, 105, 106, 115, 116, 117, 118,
40: 119}
40: excls[117][1378..1394]={102, 104, 105, 106, 115, 116, 117, 118,
40: 119, 120, 121, 122, 123, 124, 134, 135, 136}
40: excls[118][1395..1403]={104, 115, 116, 117, 118, 119, 120, 121,
40: 134}
40: excls[119][1404..1422]={104, 115, 116, 117, 118, 119, 120, 121,
40: 122, 123, 124, 125, 126, 130, 134, 135, 136, 137, 138}
40: excls[120][1423..1434]={115, 117, 118, 119, 120, 121, 122, 123,
40: 124, 134, 135, 136}
40: excls[121][1435..1455]={115, 117, 118, 119, 120, 121, 122, 123,
40: 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135,
40: 136}
40: excls[122][1456..1466]={117, 119, 120, 121, 122, 123, 124, 125,
40: 126, 130, 134}
40: excls[123][1467..1477]={117, 119, 120, 121, 122, 123, 124, 125,
40: 126, 130, 134}
40: excls[124][1478..1494]={117, 119, 120, 121, 122, 123, 124, 125,
40: 126, 127, 128, 129, 130, 131, 132, 133, 134}
40: excls[125][1495..1508]={119, 121, 122, 123, 124, 125, 126, 127,
40: 128, 129, 130, 131, 132, 133}
40: excls[126][1509..1522]={119, 121, 122, 123, 124, 125, 126, 127,
40: 128, 129, 130, 131, 132, 133}
40: excls[127][1523..1530]={121, 124, 125, 126, 127, 128, 129, 130}
40: excls[128][1531..1538]={121, 124, 125, 126, 127, 128, 129, 130}
40: excls[129][1539..1546]={121, 124, 125, 126, 127, 128, 129, 130}
40: excls[130][1547..1560]={119, 121, 122, 123, 124, 125, 126, 127,
40: 128, 129, 130, 131, 132, 133}
40: excls[131][1561..1568]={121, 124, 125, 126, 130, 131, 132, 133}
40: excls[132][1569..1576]={121, 124, 125, 126, 130, 131, 132, 133}
40: excls[133][1577..1584]={121, 124, 125, 126, 130, 131, 132, 133}
40: excls[134][1585..1601]={115, 117, 118, 119, 120, 121, 122, 123,
40: 124, 134, 135, 136, 137, 138, 139, 140, 144}
40: excls[135][1602..1610]={117, 119, 120, 121, 134, 135, 136, 137,
40: 138}
40: excls[136][1611..1627]={117, 119, 120, 121, 134, 135, 136, 137,
40: 138, 139, 140, 141, 142, 143, 144, 145, 146}
40: excls[137][1628..1636]={119, 134, 135, 136, 137, 138, 139, 140,
40: 144}
40: excls[138][1637..1652]={119, 134, 135, 136, 137, 138, 139, 140,
40: 141, 142, 143, 144, 145, 146, 147, 148}
40: excls[139][1653..1664]={134, 136, 137, 138, 139, 140, 141, 142,
40: 143, 144, 145, 146}
40: excls[140][1665..1676]={134, 136, 137, 138, 139, 140, 141, 142,
40: 143, 144, 145, 146}
40: excls[141][1677..1684]={136, 138, 139, 140, 141, 142, 143, 144}
40: excls[142][1685..1692]={136, 138, 139, 140, 141, 142, 143, 144}
40: excls[143][1693..1700]={136, 138, 139, 140, 141, 142, 143, 144}
40: excls[144][1701..1717]={134, 136, 137, 138, 139, 140, 141, 142,
40: 143, 144, 145, 146, 147, 148, 149, 150, 154}
40: excls[145][1718..1726]={136, 138, 139, 140, 144, 145, 146, 147,
40: 148}
40: excls[146][1727..1742]={136, 138, 139, 140, 144, 145, 146, 147,
40: 148, 149, 150, 151, 152, 153, 154, 155}
40: excls[147][1743..1751]={138, 144, 145, 146, 147, 148, 149, 150,
40: 154}
40: excls[148][1752..1764]={138, 144, 145, 146, 147, 148, 149, 150,
40: 151, 152, 153, 154, 155}
40: excls[149][1765..1775]={144, 146, 147, 148, 149, 150, 151, 152,
40: 153, 154, 155}
40: excls[150][1776..1786]={144, 146, 147, 148, 149, 150, 151, 152,
40: 153, 154, 155}
40: excls[151][1787..1794]={146, 148, 149, 150, 151, 152, 153, 154}
40: excls[152][1795..1802]={146, 148, 149, 150, 151, 152, 153, 154}
40: excls[153][1803..1810]={146, 148, 149, 150, 151, 152, 153, 154}
40: excls[154][1811..1821]={144, 146, 147, 148, 149, 150, 151, 152,
40: 153, 154, 155}
40: excls[155][1822..1827]={146, 148, 149, 150, 154, 155}
40: Bond:
40: nr: 468
40: iatoms:
40: 0 type=100 (BONDS) 0 1
40: 1 type=100 (BONDS) 0 2
40: 2 type=100 (BONDS) 0 3
40: 3 type=101 (BONDS) 0 4
40: 4 type=102 (BONDS) 4 5
40: 5 type=103 (BONDS) 4 6
40: 6 type=104 (BONDS) 4 22
40: 7 type=102 (BONDS) 6 7
40: 8 type=102 (BONDS) 6 8
40: 9 type=103 (BONDS) 6 9
40: 10 type=102 (BONDS) 9 10
40: 11 type=102 (BONDS) 9 11
40: 12 type=103 (BONDS) 9 12
40: 13 type=102 (BONDS) 12 13
40: 14 type=102 (BONDS) 12 14
40: 15 type=103 (BONDS) 12 15
40: 16 type=102 (BONDS) 15 16
40: 17 type=102 (BONDS) 15 17
40: 18 type=101 (BONDS) 15 18
40: 19 type=100 (BONDS) 18 19
40: 20 type=100 (BONDS) 18 20
40: 21 type=100 (BONDS) 18 21
40: 22 type=105 (BONDS) 22 23
40: 23 type=106 (BONDS) 22 24
40: 24 type=100 (BONDS) 24 25
40: 25 type=107 (BONDS) 24 26
40: 26 type=102 (BONDS) 26 27
40: 27 type=103 (BONDS) 26 28
40: 28 type=104 (BONDS) 26 38
40: 29 type=102 (BONDS) 28 29
40: 30 type=103 (BONDS) 28 30
40: 31 type=103 (BONDS) 28 34
40: 32 type=102 (BONDS) 30 31
40: 33 type=102 (BONDS) 30 32
40: 34 type=102 (BONDS) 30 33
40: 35 type=102 (BONDS) 34 35
40: 36 type=102 (BONDS) 34 36
40: 37 type=102 (BONDS) 34 37
40: 38 type=105 (BONDS) 38 39
40: 39 type=106 (BONDS) 38 40
40: 40 type=100 (BONDS) 40 41
40: 41 type=107 (BONDS) 40 42
40: 42 type=102 (BONDS) 42 43
40: 43 type=103 (BONDS) 42 44
40: 44 type=104 (BONDS) 42 58
40: 45 type=102 (BONDS) 44 45
40: 46 type=102 (BONDS) 44 46
40: 47 type=108 (BONDS) 44 47
40: 48 type=109 (BONDS) 47 48
40: 49 type=109 (BONDS) 47 50
40: 50 type=110 (BONDS) 48 49
40: 51 type=109 (BONDS) 48 52
40: 52 type=110 (BONDS) 50 51
40: 53 type=109 (BONDS) 50 54
40: 54 type=110 (BONDS) 52 53
40: 55 type=109 (BONDS) 52 56
40: 56 type=110 (BONDS) 54 55
40: 57 type=109 (BONDS) 54 56
40: 58 type=110 (BONDS) 56 57
40: 59 type=105 (BONDS) 58 59
40: 60 type=106 (BONDS) 58 60
40: 61 type=100 (BONDS) 60 61
40: 62 type=107 (BONDS) 60 62
40: 63 type=102 (BONDS) 62 63
40: 64 type=102 (BONDS) 62 64
40: 65 type=104 (BONDS) 62 65
40: 66 type=105 (BONDS) 65 66
40: 67 type=106 (BONDS) 65 67
40: 68 type=100 (BONDS) 67 68
40: 69 type=107 (BONDS) 67 69
40: 70 type=102 (BONDS) 69 70
40: 71 type=103 (BONDS) 69 71
40: 72 type=104 (BONDS) 69 89
40: 73 type=102 (BONDS) 71 72
40: 74 type=102 (BONDS) 71 73
40: 75 type=103 (BONDS) 71 74
40: 76 type=102 (BONDS) 74 75
40: 77 type=102 (BONDS) 74 76
40: 78 type=103 (BONDS) 74 77
40: 79 type=102 (BONDS) 77 78
40: 80 type=102 (BONDS) 77 79
40: 81 type=111 (BONDS) 77 80
40: 82 type=100 (BONDS) 80 81
40: 83 type=112 (BONDS) 80 82
40: 84 type=112 (BONDS) 82 83
40: 85 type=112 (BONDS) 82 86
40: 86 type=100 (BONDS) 83 84
40: 87 type=100 (BONDS) 83 85
40: 88 type=100 (BONDS) 86 87
40: 89 type=100 (BONDS) 86 88
40: 90 type=105 (BONDS) 89 90
40: 91 type=106 (BONDS) 89 91
40: 92 type=100 (BONDS) 91 92
40: 93 type=107 (BONDS) 91 93
40: 94 type=102 (BONDS) 93 94
40: 95 type=103 (BONDS) 93 95
40: 96 type=104 (BONDS) 93 100
40: 97 type=102 (BONDS) 95 96
40: 98 type=102 (BONDS) 95 97
40: 99 type=113 (BONDS) 95 98
40: 100 type=114 (BONDS) 98 99
40: 101 type=105 (BONDS) 100 101
40: 102 type=106 (BONDS) 100 102
40: 103 type=100 (BONDS) 102 103
40: 104 type=107 (BONDS) 102 104
40: 105 type=102 (BONDS) 104 105
40: 106 type=103 (BONDS) 104 106
40: 107 type=104 (BONDS) 104 115
40: 108 type=102 (BONDS) 106 107
40: 109 type=102 (BONDS) 106 108
40: 110 type=103 (BONDS) 106 109
40: 111 type=102 (BONDS) 109 110
40: 112 type=102 (BONDS) 109 111
40: 113 type=104 (BONDS) 109 112
40: 114 type=115 (BONDS) 112 113
40: 115 type=115 (BONDS) 112 114
40: 116 type=105 (BONDS) 115 116
40: 117 type=106 (BONDS) 115 117
40: 118 type=100 (BONDS) 117 118
40: 119 type=107 (BONDS) 117 119
40: 120 type=102 (BONDS) 119 120
40: 121 type=103 (BONDS) 119 121
40: 122 type=104 (BONDS) 119 134
40: 123 type=102 (BONDS) 121 122
40: 124 type=102 (BONDS) 121 123
40: 125 type=103 (BONDS) 121 124
40: 126 type=102 (BONDS) 124 125
40: 127 type=103 (BONDS) 124 126
40: 128 type=103 (BONDS) 124 130
40: 129 type=102 (BONDS) 126 127
40: 130 type=102 (BONDS) 126 128
40: 131 type=102 (BONDS) 126 129
40: 132 type=102 (BONDS) 130 131
40: 133 type=102 (BONDS) 130 132
40: 134 type=102 (BONDS) 130 133
40: 135 type=105 (BONDS) 134 135
40: 136 type=106 (BONDS) 134 136
40: 137 type=100 (BONDS) 136 137
40: 138 type=107 (BONDS) 136 138
40: 139 type=102 (BONDS) 138 139
40: 140 type=103 (BONDS) 138 140
40: 141 type=104 (BONDS) 138 144
40: 142 type=102 (BONDS) 140 141
40: 143 type=102 (BONDS) 140 142
40: 144 type=102 (BONDS) 140 143
40: 145 type=105 (BONDS) 144 145
40: 146 type=106 (BONDS) 144 146
40: 147 type=100 (BONDS) 146 147
40: 148 type=107 (BONDS) 146 148
40: 149 type=102 (BONDS) 148 149
40: 150 type=103 (BONDS) 148 150
40: 151 type=104 (BONDS) 148 154
40: 152 type=102 (BONDS) 150 151
40: 153 type=102 (BONDS) 150 152
40: 154 type=102 (BONDS) 150 153
40: 155 type=105 (BONDS) 154 155
40: G96Bond:
40: nr: 0
40: Morse:
40: nr: 0
40: Cubic Bonds:
40: nr: 0
40: Connect Bonds:
40: nr: 0
40: Harmonic Pot.:
40: nr: 0
40: FENE Bonds:
40: nr: 0
40: Tab. Bonds:
40: nr: 0
40: Tab. Bonds NC:
40: nr: 0
40: Restraint Pot.:
40: nr: 0
40: Angle:
40: nr: 1124
40: iatoms:
40: 0 type=116 (ANGLES) 1 0 2
40: 1 type=116 (ANGLES) 1 0 3
40: 2 type=116 (ANGLES) 1 0 4
40: 3 type=116 (ANGLES) 2 0 3
40: 4 type=116 (ANGLES) 2 0 4
40: 5 type=116 (ANGLES) 3 0 4
40: 6 type=116 (ANGLES) 0 4 5
40: 7 type=117 (ANGLES) 0 4 6
40: 8 type=117 (ANGLES) 0 4 22
40: 9 type=118 (ANGLES) 5 4 6
40: 10 type=116 (ANGLES) 5 4 22
40: 11 type=119 (ANGLES) 6 4 22
40: 12 type=118 (ANGLES) 4 6 7
40: 13 type=118 (ANGLES) 4 6 8
40: 14 type=120 (ANGLES) 4 6 9
40: 15 type=121 (ANGLES) 7 6 8
40: 16 type=118 (ANGLES) 7 6 9
40: 17 type=118 (ANGLES) 8 6 9
40: 18 type=118 (ANGLES) 6 9 10
40: 19 type=118 (ANGLES) 6 9 11
40: 20 type=120 (ANGLES) 6 9 12
40: 21 type=121 (ANGLES) 10 9 11
40: 22 type=118 (ANGLES) 10 9 12
40: 23 type=118 (ANGLES) 11 9 12
40: 24 type=118 (ANGLES) 9 12 13
40: 25 type=118 (ANGLES) 9 12 14
40: 26 type=120 (ANGLES) 9 12 15
40: 27 type=121 (ANGLES) 13 12 14
40: 28 type=118 (ANGLES) 13 12 15
40: 29 type=118 (ANGLES) 14 12 15
40: 30 type=118 (ANGLES) 12 15 16
40: 31 type=118 (ANGLES) 12 15 17
40: 32 type=117 (ANGLES) 12 15 18
40: 33 type=121 (ANGLES) 16 15 17
40: 34 type=116 (ANGLES) 16 15 18
40: 35 type=116 (ANGLES) 17 15 18
40: 36 type=116 (ANGLES) 15 18 19
40: 37 type=116 (ANGLES) 15 18 20
40: 38 type=116 (ANGLES) 15 18 21
40: 39 type=116 (ANGLES) 19 18 20
40: 40 type=116 (ANGLES) 19 18 21
40: 41 type=116 (ANGLES) 20 18 21
40: 42 type=122 (ANGLES) 4 22 23
40: 43 type=123 (ANGLES) 4 22 24
40: 44 type=124 (ANGLES) 23 22 24
40: 45 type=125 (ANGLES) 22 24 25
40: 46 type=126 (ANGLES) 22 24 26
40: 47 type=127 (ANGLES) 25 24 26
40: 48 type=116 (ANGLES) 24 26 27
40: 49 type=128 (ANGLES) 24 26 28
40: 50 type=129 (ANGLES) 24 26 38
40: 51 type=118 (ANGLES) 27 26 28
40: 52 type=116 (ANGLES) 27 26 38
40: 53 type=119 (ANGLES) 28 26 38
40: 54 type=118 (ANGLES) 26 28 29
40: 55 type=120 (ANGLES) 26 28 30
40: 56 type=120 (ANGLES) 26 28 34
40: 57 type=118 (ANGLES) 29 28 30
40: 58 type=118 (ANGLES) 29 28 34
40: 59 type=120 (ANGLES) 30 28 34
40: 60 type=118 (ANGLES) 28 30 31
40: 61 type=118 (ANGLES) 28 30 32
40: 62 type=118 (ANGLES) 28 30 33
40: 63 type=121 (ANGLES) 31 30 32
40: 64 type=121 (ANGLES) 31 30 33
40: 65 type=121 (ANGLES) 32 30 33
40: 66 type=118 (ANGLES) 28 34 35
40: 67 type=118 (ANGLES) 28 34 36
40: 68 type=118 (ANGLES) 28 34 37
40: 69 type=121 (ANGLES) 35 34 36
40: 70 type=121 (ANGLES) 35 34 37
40: 71 type=121 (ANGLES) 36 34 37
40: 72 type=122 (ANGLES) 26 38 39
40: 73 type=123 (ANGLES) 26 38 40
40: 74 type=124 (ANGLES) 39 38 40
40: 75 type=125 (ANGLES) 38 40 41
40: 76 type=126 (ANGLES) 38 40 42
40: 77 type=127 (ANGLES) 41 40 42
40: 78 type=116 (ANGLES) 40 42 43
40: 79 type=128 (ANGLES) 40 42 44
40: 80 type=129 (ANGLES) 40 42 58
40: 81 type=118 (ANGLES) 43 42 44
40: 82 type=116 (ANGLES) 43 42 58
40: 83 type=119 (ANGLES) 44 42 58
40: 84 type=118 (ANGLES) 42 44 45
40: 85 type=118 (ANGLES) 42 44 46
40: 86 type=130 (ANGLES) 42 44 47
40: 87 type=121 (ANGLES) 45 44 46
40: 88 type=116 (ANGLES) 45 44 47
40: 89 type=116 (ANGLES) 46 44 47
40: 90 type=131 (ANGLES) 44 47 48
40: 91 type=131 (ANGLES) 44 47 50
40: 92 type=132 (ANGLES) 48 47 50
40: 93 type=133 (ANGLES) 47 48 49
40: 94 type=132 (ANGLES) 47 48 52
40: 95 type=133 (ANGLES) 49 48 52
40: 96 type=133 (ANGLES) 47 50 51
40: 97 type=132 (ANGLES) 47 50 54
40: 98 type=133 (ANGLES) 51 50 54
40: 99 type=133 (ANGLES) 48 52 53
40: 100 type=132 (ANGLES) 48 52 56
40: 101 type=133 (ANGLES) 53 52 56
40: 102 type=133 (ANGLES) 50 54 55
40: 103 type=132 (ANGLES) 50 54 56
40: 104 type=133 (ANGLES) 55 54 56
40: 105 type=132 (ANGLES) 52 56 54
40: 106 type=133 (ANGLES) 52 56 57
40: 107 type=133 (ANGLES) 54 56 57
40: 108 type=122 (ANGLES) 42 58 59
40: 109 type=123 (ANGLES) 42 58 60
40: 110 type=124 (ANGLES) 59 58 60
40: 111 type=125 (ANGLES) 58 60 61
40: 112 type=126 (ANGLES) 58 60 62
40: 113 type=127 (ANGLES) 61 60 62
40: 114 type=116 (ANGLES) 60 62 63
40: 115 type=116 (ANGLES) 60 62 64
40: 116 type=129 (ANGLES) 60 62 65
40: 117 type=121 (ANGLES) 63 62 64
40: 118 type=116 (ANGLES) 63 62 65
40: 119 type=116 (ANGLES) 64 62 65
40: 120 type=122 (ANGLES) 62 65 66
40: 121 type=123 (ANGLES) 62 65 67
40: 122 type=124 (ANGLES) 66 65 67
40: 123 type=125 (ANGLES) 65 67 68
40: 124 type=126 (ANGLES) 65 67 69
40: 125 type=127 (ANGLES) 68 67 69
40: 126 type=116 (ANGLES) 67 69 70
40: 127 type=128 (ANGLES) 67 69 71
40: 128 type=129 (ANGLES) 67 69 89
40: 129 type=118 (ANGLES) 70 69 71
40: 130 type=116 (ANGLES) 70 69 89
40: 131 type=119 (ANGLES) 71 69 89
40: 132 type=118 (ANGLES) 69 71 72
40: 133 type=118 (ANGLES) 69 71 73
40: 134 type=120 (ANGLES) 69 71 74
40: 135 type=121 (ANGLES) 72 71 73
40: 136 type=118 (ANGLES) 72 71 74
40: 137 type=118 (ANGLES) 73 71 74
40: 138 type=118 (ANGLES) 71 74 75
40: 139 type=118 (ANGLES) 71 74 76
40: 140 type=120 (ANGLES) 71 74 77
40: 141 type=121 (ANGLES) 75 74 76
40: 142 type=118 (ANGLES) 75 74 77
40: 143 type=118 (ANGLES) 76 74 77
40: 144 type=118 (ANGLES) 74 77 78
40: 145 type=118 (ANGLES) 74 77 79
40: 146 type=117 (ANGLES) 74 77 80
40: 147 type=121 (ANGLES) 78 77 79
40: 148 type=116 (ANGLES) 78 77 80
40: 149 type=116 (ANGLES) 79 77 80
40: 150 type=134 (ANGLES) 77 80 81
40: 151 type=135 (ANGLES) 77 80 82
40: 152 type=133 (ANGLES) 81 80 82
40: 153 type=131 (ANGLES) 80 82 83
40: 154 type=131 (ANGLES) 80 82 86
40: 155 type=131 (ANGLES) 83 82 86
40: 156 type=133 (ANGLES) 82 83 84
40: 157 type=133 (ANGLES) 82 83 85
40: 158 type=133 (ANGLES) 84 83 85
40: 159 type=133 (ANGLES) 82 86 87
40: 160 type=133 (ANGLES) 82 86 88
40: 161 type=133 (ANGLES) 87 86 88
40: 162 type=122 (ANGLES) 69 89 90
40: 163 type=123 (ANGLES) 69 89 91
40: 164 type=124 (ANGLES) 90 89 91
40: 165 type=125 (ANGLES) 89 91 92
40: 166 type=126 (ANGLES) 89 91 93
40: 167 type=127 (ANGLES) 92 91 93
40: 168 type=116 (ANGLES) 91 93 94
40: 169 type=128 (ANGLES) 91 93 95
40: 170 type=129 (ANGLES) 91 93 100
40: 171 type=118 (ANGLES) 94 93 95
40: 172 type=116 (ANGLES) 94 93 100
40: 173 type=119 (ANGLES) 95 93 100
40: 174 type=118 (ANGLES) 93 95 96
40: 175 type=118 (ANGLES) 93 95 97
40: 176 type=136 (ANGLES) 93 95 98
40: 177 type=121 (ANGLES) 96 95 97
40: 178 type=116 (ANGLES) 96 95 98
40: 179 type=116 (ANGLES) 97 95 98
40: 180 type=137 (ANGLES) 95 98 99
40: 181 type=122 (ANGLES) 93 100 101
40: 182 type=123 (ANGLES) 93 100 102
40: 183 type=124 (ANGLES) 101 100 102
40: 184 type=125 (ANGLES) 100 102 103
40: 185 type=126 (ANGLES) 100 102 104
40: 186 type=127 (ANGLES) 103 102 104
40: 187 type=116 (ANGLES) 102 104 105
40: 188 type=128 (ANGLES) 102 104 106
40: 189 type=129 (ANGLES) 102 104 115
40: 190 type=118 (ANGLES) 105 104 106
40: 191 type=116 (ANGLES) 105 104 115
40: 192 type=119 (ANGLES) 106 104 115
40: 193 type=118 (ANGLES) 104 106 107
40: 194 type=118 (ANGLES) 104 106 108
40: 195 type=120 (ANGLES) 104 106 109
40: 196 type=121 (ANGLES) 107 106 108
40: 197 type=118 (ANGLES) 107 106 109
40: 198 type=118 (ANGLES) 108 106 109
40: 199 type=118 (ANGLES) 106 109 110
40: 200 type=118 (ANGLES) 106 109 111
40: 201 type=119 (ANGLES) 106 109 112
40: 202 type=121 (ANGLES) 110 109 111
40: 203 type=116 (ANGLES) 110 109 112
40: 204 type=116 (ANGLES) 111 109 112
40: 205 type=138 (ANGLES) 109 112 113
40: 206 type=138 (ANGLES) 109 112 114
40: 207 type=139 (ANGLES) 113 112 114
40: 208 type=122 (ANGLES) 104 115 116
40: 209 type=123 (ANGLES) 104 115 117
40: 210 type=124 (ANGLES) 116 115 117
40: 211 type=125 (ANGLES) 115 117 118
40: 212 type=126 (ANGLES) 115 117 119
40: 213 type=127 (ANGLES) 118 117 119
40: 214 type=116 (ANGLES) 117 119 120
40: 215 type=128 (ANGLES) 117 119 121
40: 216 type=129 (ANGLES) 117 119 134
40: 217 type=118 (ANGLES) 120 119 121
40: 218 type=116 (ANGLES) 120 119 134
40: 219 type=119 (ANGLES) 121 119 134
40: 220 type=118 (ANGLES) 119 121 122
40: 221 type=118 (ANGLES) 119 121 123
40: 222 type=120 (ANGLES) 119 121 124
40: 223 type=121 (ANGLES) 122 121 123
40: 224 type=118 (ANGLES) 122 121 124
40: 225 type=118 (ANGLES) 123 121 124
40: 226 type=118 (ANGLES) 121 124 125
40: 227 type=120 (ANGLES) 121 124 126
40: 228 type=120 (ANGLES) 121 124 130
40: 229 type=118 (ANGLES) 125 124 126
40: 230 type=118 (ANGLES) 125 124 130
40: 231 type=120 (ANGLES) 126 124 130
40: 232 type=118 (ANGLES) 124 126 127
40: 233 type=118 (ANGLES) 124 126 128
40: 234 type=118 (ANGLES) 124 126 129
40: 235 type=121 (ANGLES) 127 126 128
40: 236 type=121 (ANGLES) 127 126 129
40: 237 type=121 (ANGLES) 128 126 129
40: 238 type=118 (ANGLES) 124 130 131
40: 239 type=118 (ANGLES) 124 130 132
40: 240 type=118 (ANGLES) 124 130 133
40: 241 type=121 (ANGLES) 131 130 132
40: 242 type=121 (ANGLES) 131 130 133
40: 243 type=121 (ANGLES) 132 130 133
40: 244 type=122 (ANGLES) 119 134 135
40: 245 type=123 (ANGLES) 119 134 136
40: 246 type=124 (ANGLES) 135 134 136
40: 247 type=125 (ANGLES) 134 136 137
40: 248 type=126 (ANGLES) 134 136 138
40: 249 type=127 (ANGLES) 137 136 138
40: 250 type=116 (ANGLES) 136 138 139
40: 251 type=128 (ANGLES) 136 138 140
40: 252 type=129 (ANGLES) 136 138 144
40: 253 type=118 (ANGLES) 139 138 140
40: 254 type=116 (ANGLES) 139 138 144
40: 255 type=119 (ANGLES) 140 138 144
40: 256 type=118 (ANGLES) 138 140 141
40: 257 type=118 (ANGLES) 138 140 142
40: 258 type=118 (ANGLES) 138 140 143
40: 259 type=121 (ANGLES) 141 140 142
40: 260 type=121 (ANGLES) 141 140 143
40: 261 type=121 (ANGLES) 142 140 143
40: 262 type=122 (ANGLES) 138 144 145
40: 263 type=123 (ANGLES) 138 144 146
40: 264 type=124 (ANGLES) 145 144 146
40: 265 type=125 (ANGLES) 144 146 147
40: 266 type=126 (ANGLES) 144 146 148
40: 267 type=127 (ANGLES) 147 146 148
40: 268 type=116 (ANGLES) 146 148 149
40: 269 type=128 (ANGLES) 146 148 150
40: 270 type=129 (ANGLES) 146 148 154
40: 271 type=118 (ANGLES) 149 148 150
40: 272 type=116 (ANGLES) 149 148 154
40: 273 type=119 (ANGLES) 150 148 154
40: 274 type=118 (ANGLES) 148 150 151
40: 275 type=118 (ANGLES) 148 150 152
40: 276 type=118 (ANGLES) 148 150 153
40: 277 type=121 (ANGLES) 151 150 152
40: 278 type=121 (ANGLES) 151 150 153
40: 279 type=121 (ANGLES) 152 150 153
40: 280 type=122 (ANGLES) 148 154 155
40: G96Angle:
40: nr: 0
40: Restricted Angles:
40: nr: 0
40: Lin. Angle:
40: nr: 0
40: Bond-Cross:
40: nr: 0
40: BA-Cross:
40: nr: 0
40: U-B:
40: nr: 0
40: Quartic Angles:
40: nr: 0
40: Tab. Angles:
40: nr: 0
40: Proper Dih.:
40: nr: 145
40: iatoms:
40: 0 type=140 (PDIHS) 4 24 22 23
40: 1 type=141 (PDIHS) 22 26 24 25
40: 2 type=140 (PDIHS) 26 40 38 39
40: 3 type=141 (PDIHS) 38 42 40 41
40: 4 type=140 (PDIHS) 42 60 58 59
40: 5 type=142 (PDIHS) 44 47 50 48
40: 6 type=142 (PDIHS) 47 52 48 49
40: 7 type=142 (PDIHS) 47 54 50 51
40: 8 type=142 (PDIHS) 48 56 52 53
40: 9 type=142 (PDIHS) 50 56 54 55
40: 10 type=142 (PDIHS) 52 54 56 57
40: 11 type=141 (PDIHS) 58 62 60 61
40: 12 type=140 (PDIHS) 62 67 65 66
40: 13 type=141 (PDIHS) 65 69 67 68
40: 14 type=140 (PDIHS) 69 91 89 90
40: 15 type=141 (PDIHS) 77 82 80 81
40: 16 type=140 (PDIHS) 80 83 82 86
40: 17 type=141 (PDIHS) 82 84 83 85
40: 18 type=141 (PDIHS) 82 87 86 88
40: 19 type=141 (PDIHS) 89 93 91 92
40: 20 type=140 (PDIHS) 93 102 100 101
40: 21 type=141 (PDIHS) 100 104 102 103
40: 22 type=140 (PDIHS) 104 117 115 116
40: 23 type=140 (PDIHS) 109 113 112 114
40: 24 type=141 (PDIHS) 115 119 117 118
40: 25 type=140 (PDIHS) 119 136 134 135
40: 26 type=141 (PDIHS) 134 138 136 137
40: 27 type=140 (PDIHS) 138 146 144 145
40: 28 type=141 (PDIHS) 144 148 146 147
40: Ryckaert-Bell.:
40: nr: 1565
40: iatoms:
40: 0 type=143 (RBDIHS) 1 0 4 5
40: 1 type=144 (RBDIHS) 1 0 4 6
40: 2 type=144 (RBDIHS) 1 0 4 22
40: 3 type=143 (RBDIHS) 2 0 4 5
40: 4 type=144 (RBDIHS) 2 0 4 6
40: 5 type=144 (RBDIHS) 2 0 4 22
40: 6 type=143 (RBDIHS) 3 0 4 5
40: 7 type=144 (RBDIHS) 3 0 4 6
40: 8 type=144 (RBDIHS) 3 0 4 22
40: 9 type=145 (RBDIHS) 0 4 6 9
40: 10 type=146 (RBDIHS) 22 4 6 9
40: 11 type=147 (RBDIHS) 0 4 6 7
40: 12 type=147 (RBDIHS) 0 4 6 8
40: 13 type=148 (RBDIHS) 5 4 6 7
40: 14 type=148 (RBDIHS) 5 4 6 8
40: 15 type=148 (RBDIHS) 5 4 6 9
40: 16 type=149 (RBDIHS) 22 4 6 7
40: 17 type=149 (RBDIHS) 22 4 6 8
40: 18 type=150 (RBDIHS) 0 4 22 24
40: 19 type=151 (RBDIHS) 6 4 22 24
40: 20 type=148 (RBDIHS) 4 6 9 10
40: 21 type=148 (RBDIHS) 4 6 9 11
40: 22 type=152 (RBDIHS) 4 6 9 12
40: 23 type=148 (RBDIHS) 7 6 9 10
40: 24 type=148 (RBDIHS) 7 6 9 11
40: 25 type=148 (RBDIHS) 7 6 9 12
40: 26 type=148 (RBDIHS) 8 6 9 10
40: 27 type=148 (RBDIHS) 8 6 9 11
40: 28 type=148 (RBDIHS) 8 6 9 12
40: 29 type=148 (RBDIHS) 6 9 12 13
40: 30 type=148 (RBDIHS) 6 9 12 14
40: 31 type=152 (RBDIHS) 6 9 12 15
40: 32 type=148 (RBDIHS) 10 9 12 13
40: 33 type=148 (RBDIHS) 10 9 12 14
40: 34 type=148 (RBDIHS) 10 9 12 15
40: 35 type=148 (RBDIHS) 11 9 12 13
40: 36 type=148 (RBDIHS) 11 9 12 14
40: 37 type=148 (RBDIHS) 11 9 12 15
40: 38 type=148 (RBDIHS) 9 12 15 16
40: 39 type=148 (RBDIHS) 9 12 15 17
40: 40 type=153 (RBDIHS) 9 12 15 18
40: 41 type=148 (RBDIHS) 13 12 15 16
40: 42 type=148 (RBDIHS) 13 12 15 17
40: 43 type=154 (RBDIHS) 13 12 15 18
40: 44 type=148 (RBDIHS) 14 12 15 16
40: 45 type=148 (RBDIHS) 14 12 15 17
40: 46 type=154 (RBDIHS) 14 12 15 18
40: 47 type=144 (RBDIHS) 12 15 18 19
40: 48 type=144 (RBDIHS) 12 15 18 20
40: 49 type=144 (RBDIHS) 12 15 18 21
40: 50 type=143 (RBDIHS) 16 15 18 19
40: 51 type=143 (RBDIHS) 16 15 18 20
40: 52 type=143 (RBDIHS) 16 15 18 21
40: 53 type=143 (RBDIHS) 17 15 18 19
40: 54 type=143 (RBDIHS) 17 15 18 20
40: 55 type=143 (RBDIHS) 17 15 18 21
40: 56 type=155 (RBDIHS) 4 22 24 25
40: 57 type=156 (RBDIHS) 4 22 24 26
40: 58 type=155 (RBDIHS) 23 22 24 25
40: 59 type=157 (RBDIHS) 23 22 24 26
40: 60 type=158 (RBDIHS) 22 24 26 28
40: 61 type=159 (RBDIHS) 22 24 26 38
40: 62 type=160 (RBDIHS) 24 26 28 30
40: 63 type=160 (RBDIHS) 24 26 28 34
40: 64 type=161 (RBDIHS) 38 26 28 30
40: 65 type=161 (RBDIHS) 38 26 28 34
40: 66 type=147 (RBDIHS) 24 26 28 29
40: 67 type=148 (RBDIHS) 27 26 28 29
40: 68 type=148 (RBDIHS) 27 26 28 30
40: 69 type=148 (RBDIHS) 27 26 28 34
40: 70 type=149 (RBDIHS) 38 26 28 29
40: 71 type=150 (RBDIHS) 24 26 38 40
40: 72 type=151 (RBDIHS) 28 26 38 40
40: 73 type=148 (RBDIHS) 26 28 30 31
40: 74 type=148 (RBDIHS) 26 28 30 32
40: 75 type=148 (RBDIHS) 26 28 30 33
40: 76 type=148 (RBDIHS) 29 28 30 31
40: 77 type=148 (RBDIHS) 29 28 30 32
40: 78 type=148 (RBDIHS) 29 28 30 33
40: 79 type=148 (RBDIHS) 34 28 30 31
40: 80 type=148 (RBDIHS) 34 28 30 32
40: 81 type=148 (RBDIHS) 34 28 30 33
40: 82 type=148 (RBDIHS) 26 28 34 35
40: 83 type=148 (RBDIHS) 26 28 34 36
40: 84 type=148 (RBDIHS) 26 28 34 37
40: 85 type=148 (RBDIHS) 29 28 34 35
40: 86 type=148 (RBDIHS) 29 28 34 36
40: 87 type=148 (RBDIHS) 29 28 34 37
40: 88 type=148 (RBDIHS) 30 28 34 35
40: 89 type=148 (RBDIHS) 30 28 34 36
40: 90 type=148 (RBDIHS) 30 28 34 37
40: 91 type=155 (RBDIHS) 26 38 40 41
40: 92 type=156 (RBDIHS) 26 38 40 42
40: 93 type=155 (RBDIHS) 39 38 40 41
40: 94 type=157 (RBDIHS) 39 38 40 42
40: 95 type=158 (RBDIHS) 38 40 42 44
40: 96 type=159 (RBDIHS) 38 40 42 58
40: 97 type=147 (RBDIHS) 40 42 44 45
40: 98 type=147 (RBDIHS) 40 42 44 46
40: 99 type=162 (RBDIHS) 40 42 44 47
40: 100 type=148 (RBDIHS) 43 42 44 45
40: 101 type=148 (RBDIHS) 43 42 44 46
40: 102 type=163 (RBDIHS) 43 42 44 47
40: 103 type=149 (RBDIHS) 58 42 44 45
40: 104 type=149 (RBDIHS) 58 42 44 46
40: 105 type=164 (RBDIHS) 58 42 44 47
40: 106 type=150 (RBDIHS) 40 42 58 60
40: 107 type=151 (RBDIHS) 44 42 58 60
40: 108 type=165 (RBDIHS) 44 47 48 49
40: 109 type=165 (RBDIHS) 44 47 48 52
40: 110 type=165 (RBDIHS) 50 47 48 49
40: 111 type=165 (RBDIHS) 50 47 48 52
40: 112 type=165 (RBDIHS) 44 47 50 51
40: 113 type=165 (RBDIHS) 44 47 50 54
40: 114 type=165 (RBDIHS) 48 47 50 51
40: 115 type=165 (RBDIHS) 48 47 50 54
40: 116 type=165 (RBDIHS) 47 48 52 53
40: 117 type=165 (RBDIHS) 47 48 52 56
40: 118 type=165 (RBDIHS) 49 48 52 53
40: 119 type=165 (RBDIHS) 49 48 52 56
40: 120 type=165 (RBDIHS) 47 50 54 55
40: 121 type=165 (RBDIHS) 47 50 54 56
40: 122 type=165 (RBDIHS) 51 50 54 55
40: 123 type=165 (RBDIHS) 51 50 54 56
40: 124 type=165 (RBDIHS) 48 52 56 54
40: 125 type=165 (RBDIHS) 48 52 56 57
40: 126 type=165 (RBDIHS) 53 52 56 54
40: 127 type=165 (RBDIHS) 53 52 56 57
40: 128 type=165 (RBDIHS) 50 54 56 52
40: 129 type=165 (RBDIHS) 50 54 56 57
40: 130 type=165 (RBDIHS) 55 54 56 52
40: 131 type=165 (RBDIHS) 55 54 56 57
40: 132 type=155 (RBDIHS) 42 58 60 61
40: 133 type=156 (RBDIHS) 42 58 60 62
40: 134 type=155 (RBDIHS) 59 58 60 61
40: 135 type=157 (RBDIHS) 59 58 60 62
40: 136 type=159 (RBDIHS) 58 60 62 65
40: 137 type=150 (RBDIHS) 60 62 65 67
40: 138 type=155 (RBDIHS) 62 65 67 68
40: 139 type=156 (RBDIHS) 62 65 67 69
40: 140 type=155 (RBDIHS) 66 65 67 68
40: 141 type=157 (RBDIHS) 66 65 67 69
40: 142 type=158 (RBDIHS) 65 67 69 71
40: 143 type=159 (RBDIHS) 65 67 69 89
40: 144 type=166 (RBDIHS) 67 69 71 74
40: 145 type=167 (RBDIHS) 89 69 71 74
40: 146 type=147 (RBDIHS) 67 69 71 72
40: 147 type=147 (RBDIHS) 67 69 71 73
40: 148 type=148 (RBDIHS) 70 69 71 72
40: 149 type=148 (RBDIHS) 70 69 71 73
40: 150 type=148 (RBDIHS) 70 69 71 74
40: 151 type=149 (RBDIHS) 89 69 71 72
40: 152 type=149 (RBDIHS) 89 69 71 73
40: 153 type=150 (RBDIHS) 67 69 89 91
40: 154 type=151 (RBDIHS) 71 69 89 91
40: 155 type=148 (RBDIHS) 69 71 74 75
40: 156 type=148 (RBDIHS) 69 71 74 76
40: 157 type=152 (RBDIHS) 69 71 74 77
40: 158 type=148 (RBDIHS) 72 71 74 75
40: 159 type=148 (RBDIHS) 72 71 74 76
40: 160 type=148 (RBDIHS) 72 71 74 77
40: 161 type=148 (RBDIHS) 73 71 74 75
40: 162 type=148 (RBDIHS) 73 71 74 76
40: 163 type=148 (RBDIHS) 73 71 74 77
40: 164 type=148 (RBDIHS) 71 74 77 78
40: 165 type=148 (RBDIHS) 71 74 77 79
40: 166 type=153 (RBDIHS) 71 74 77 80
40: 167 type=148 (RBDIHS) 75 74 77 78
40: 168 type=148 (RBDIHS) 75 74 77 79
40: 169 type=168 (RBDIHS) 75 74 77 80
40: 170 type=148 (RBDIHS) 76 74 77 78
40: 171 type=148 (RBDIHS) 76 74 77 79
40: 172 type=168 (RBDIHS) 76 74 77 80
40: 173 type=169 (RBDIHS) 74 77 80 81
40: 174 type=170 (RBDIHS) 74 77 80 82
40: 175 type=171 (RBDIHS) 78 77 80 82
40: 176 type=171 (RBDIHS) 79 77 80 82
40: 177 type=172 (RBDIHS) 77 80 82 83
40: 178 type=172 (RBDIHS) 77 80 82 86
40: 179 type=173 (RBDIHS) 81 80 82 83
40: 180 type=173 (RBDIHS) 81 80 82 86
40: 181 type=173 (RBDIHS) 80 82 83 84
40: 182 type=173 (RBDIHS) 80 82 83 85
40: 183 type=173 (RBDIHS) 86 82 83 84
40: 184 type=173 (RBDIHS) 86 82 83 85
40: 185 type=173 (RBDIHS) 80 82 86 87
40: 186 type=173 (RBDIHS) 80 82 86 88
40: 187 type=173 (RBDIHS) 83 82 86 87
40: 188 type=173 (RBDIHS) 83 82 86 88
40: 189 type=155 (RBDIHS) 69 89 91 92
40: 190 type=156 (RBDIHS) 69 89 91 93
40: 191 type=155 (RBDIHS) 90 89 91 92
40: 192 type=157 (RBDIHS) 90 89 91 93
40: 193 type=158 (RBDIHS) 89 91 93 95
40: 194 type=159 (RBDIHS) 89 91 93 100
40: 195 type=174 (RBDIHS) 91 93 95 98
40: 196 type=175 (RBDIHS) 100 93 95 98
40: 197 type=147 (RBDIHS) 91 93 95 96
40: 198 type=147 (RBDIHS) 91 93 95 97
40: 199 type=148 (RBDIHS) 94 93 95 96
40: 200 type=148 (RBDIHS) 94 93 95 97
40: 201 type=176 (RBDIHS) 94 93 95 98
40: 202 type=149 (RBDIHS) 100 93 95 96
40: 203 type=149 (RBDIHS) 100 93 95 97
40: 204 type=150 (RBDIHS) 91 93 100 102
40: 205 type=151 (RBDIHS) 95 93 100 102
40: 206 type=177 (RBDIHS) 93 95 98 99
40: 207 type=178 (RBDIHS) 96 95 98 99
40: 208 type=178 (RBDIHS) 97 95 98 99
40: 209 type=155 (RBDIHS) 93 100 102 103
40: 210 type=156 (RBDIHS) 93 100 102 104
40: 211 type=155 (RBDIHS) 101 100 102 103
40: 212 type=157 (RBDIHS) 101 100 102 104
40: 213 type=158 (RBDIHS) 100 102 104 106
40: 214 type=159 (RBDIHS) 100 102 104 115
40: 215 type=179 (RBDIHS) 102 104 106 109
40: 216 type=180 (RBDIHS) 115 104 106 109
40: 217 type=147 (RBDIHS) 102 104 106 107
40: 218 type=147 (RBDIHS) 102 104 106 108
40: 219 type=148 (RBDIHS) 105 104 106 107
40: 220 type=148 (RBDIHS) 105 104 106 108
40: 221 type=148 (RBDIHS) 105 104 106 109
40: 222 type=149 (RBDIHS) 115 104 106 107
40: 223 type=149 (RBDIHS) 115 104 106 108
40: 224 type=150 (RBDIHS) 102 104 115 117
40: 225 type=151 (RBDIHS) 106 104 115 117
40: 226 type=148 (RBDIHS) 104 106 109 110
40: 227 type=148 (RBDIHS) 104 106 109 111
40: 228 type=181 (RBDIHS) 104 106 109 112
40: 229 type=148 (RBDIHS) 107 106 109 110
40: 230 type=148 (RBDIHS) 107 106 109 111
40: 231 type=182 (RBDIHS) 107 106 109 112
40: 232 type=148 (RBDIHS) 108 106 109 110
40: 233 type=148 (RBDIHS) 108 106 109 111
40: 234 type=182 (RBDIHS) 108 106 109 112
40: 235 type=183 (RBDIHS) 106 109 112 113
40: 236 type=183 (RBDIHS) 106 109 112 114
40: 237 type=155 (RBDIHS) 104 115 117 118
40: 238 type=156 (RBDIHS) 104 115 117 119
40: 239 type=155 (RBDIHS) 116 115 117 118
40: 240 type=157 (RBDIHS) 116 115 117 119
40: 241 type=158 (RBDIHS) 115 117 119 121
40: 242 type=159 (RBDIHS) 115 117 119 134
40: 243 type=184 (RBDIHS) 117 119 121 124
40: 244 type=185 (RBDIHS) 134 119 121 124
40: 245 type=147 (RBDIHS) 117 119 121 122
40: 246 type=147 (RBDIHS) 117 119 121 123
40: 247 type=148 (RBDIHS) 120 119 121 122
40: 248 type=148 (RBDIHS) 120 119 121 123
40: 249 type=148 (RBDIHS) 120 119 121 124
40: 250 type=149 (RBDIHS) 134 119 121 122
40: 251 type=149 (RBDIHS) 134 119 121 123
40: 252 type=150 (RBDIHS) 117 119 134 136
40: 253 type=151 (RBDIHS) 121 119 134 136
40: 254 type=148 (RBDIHS) 119 121 124 125
40: 255 type=152 (RBDIHS) 119 121 124 126
40: 256 type=152 (RBDIHS) 119 121 124 130
40: 257 type=148 (RBDIHS) 122 121 124 125
40: 258 type=148 (RBDIHS) 122 121 124 126
40: 259 type=148 (RBDIHS) 122 121 124 130
40: 260 type=148 (RBDIHS) 123 121 124 125
40: 261 type=148 (RBDIHS) 123 121 124 126
40: 262 type=148 (RBDIHS) 123 121 124 130
40: 263 type=148 (RBDIHS) 121 124 126 127
40: 264 type=148 (RBDIHS) 121 124 126 128
40: 265 type=148 (RBDIHS) 121 124 126 129
40: 266 type=148 (RBDIHS) 125 124 126 127
40: 267 type=148 (RBDIHS) 125 124 126 128
40: 268 type=148 (RBDIHS) 125 124 126 129
40: 269 type=148 (RBDIHS) 130 124 126 127
40: 270 type=148 (RBDIHS) 130 124 126 128
40: 271 type=148 (RBDIHS) 130 124 126 129
40: 272 type=148 (RBDIHS) 121 124 130 131
40: 273 type=148 (RBDIHS) 121 124 130 132
40: 274 type=148 (RBDIHS) 121 124 130 133
40: 275 type=148 (RBDIHS) 125 124 130 131
40: 276 type=148 (RBDIHS) 125 124 130 132
40: 277 type=148 (RBDIHS) 125 124 130 133
40: 278 type=148 (RBDIHS) 126 124 130 131
40: 279 type=148 (RBDIHS) 126 124 130 132
40: 280 type=148 (RBDIHS) 126 124 130 133
40: 281 type=155 (RBDIHS) 119 134 136 137
40: 282 type=156 (RBDIHS) 119 134 136 138
40: 283 type=155 (RBDIHS) 135 134 136 137
40: 284 type=157 (RBDIHS) 135 134 136 138
40: 285 type=158 (RBDIHS) 134 136 138 140
40: 286 type=159 (RBDIHS) 134 136 138 144
40: 287 type=147 (RBDIHS) 136 138 140 141
40: 288 type=147 (RBDIHS) 136 138 140 142
40: 289 type=147 (RBDIHS) 136 138 140 143
40: 290 type=148 (RBDIHS) 139 138 140 141
40: 291 type=148 (RBDIHS) 139 138 140 142
40: 292 type=148 (RBDIHS) 139 138 140 143
40: 293 type=149 (RBDIHS) 144 138 140 141
40: 294 type=149 (RBDIHS) 144 138 140 142
40: 295 type=149 (RBDIHS) 144 138 140 143
40: 296 type=150 (RBDIHS) 136 138 144 146
40: 297 type=151 (RBDIHS) 140 138 144 146
40: 298 type=155 (RBDIHS) 138 144 146 147
40: 299 type=156 (RBDIHS) 138 144 146 148
40: 300 type=155 (RBDIHS) 145 144 146 147
40: 301 type=157 (RBDIHS) 145 144 146 148
40: 302 type=158 (RBDIHS) 144 146 148 150
40: 303 type=159 (RBDIHS) 144 146 148 154
40: 304 type=147 (RBDIHS) 146 148 150 151
40: 305 type=147 (RBDIHS) 146 148 150 152
40: 306 type=147 (RBDIHS) 146 148 150 153
40: 307 type=148 (RBDIHS) 149 148 150 151
40: 308 type=148 (RBDIHS) 149 148 150 152
40: 309 type=148 (RBDIHS) 149 148 150 153
40: 310 type=149 (RBDIHS) 154 148 150 151
40: 311 type=149 (RBDIHS) 154 148 150 152
40: 312 type=149 (RBDIHS) 154 148 150 153
40: Restricted Dih.:
40: nr: 0
40: CBT Dih.:
40: nr: 0
40: Fourier Dih.:
40: nr: 0
40: Improper Dih.:
40: nr: 0
40: Improper Dih.:
40: nr: 0
40: Tab. Dih.:
40: nr: 0
40: CMAP Dih.:
40: nr: 0
40: GB 1-2 Pol. (unused):
40: nr: 0
40: GB 1-3 Pol. (unused):
40: nr: 0
40: GB 1-4 Pol. (unused):
40: nr: 0
40: GB Polarization (unused):
40: nr: 0
40: Nonpolar Sol. (unused):
40: nr: 0
40: LJ-14:
40: nr: 1197
40: iatoms:
40: 0 type=186 (LJ14) 0 7
40: 1 type=186 (LJ14) 0 8
40: 2 type=187 (LJ14) 0 9
40: 3 type=188 (LJ14) 0 23
40: 4 type=189 (LJ14) 0 24
40: 5 type=190 (LJ14) 1 5
40: 6 type=190 (LJ14) 1 6
40: 7 type=190 (LJ14) 1 22
40: 8 type=190 (LJ14) 2 5
40: 9 type=190 (LJ14) 2 6
40: 10 type=190 (LJ14) 2 22
40: 11 type=190 (LJ14) 3 5
40: 12 type=190 (LJ14) 3 6
40: 13 type=190 (LJ14) 3 22
40: 14 type=191 (LJ14) 4 10
40: 15 type=191 (LJ14) 4 11
40: 16 type=192 (LJ14) 4 12
40: 17 type=190 (LJ14) 4 25
40: 18 type=192 (LJ14) 4 26
40: 19 type=193 (LJ14) 5 7
40: 20 type=193 (LJ14) 5 8
40: 21 type=191 (LJ14) 5 9
40: 22 type=194 (LJ14) 5 23
40: 23 type=186 (LJ14) 5 24
40: 24 type=191 (LJ14) 6 13
40: 25 type=191 (LJ14) 6 14
40: 26 type=192 (LJ14) 6 15
40: 27 type=195 (LJ14) 6 23
40: 28 type=187 (LJ14) 6 24
40: 29 type=193 (LJ14) 7 10
40: 30 type=193 (LJ14) 7 11
40: 31 type=191 (LJ14) 7 12
40: 32 type=196 (LJ14) 7 22
40: 33 type=193 (LJ14) 8 10
40: 34 type=193 (LJ14) 8 11
40: 35 type=191 (LJ14) 8 12
40: 36 type=196 (LJ14) 8 22
40: 37 type=191 (LJ14) 9 16
40: 38 type=191 (LJ14) 9 17
40: 39 type=187 (LJ14) 9 18
40: 40 type=197 (LJ14) 9 22
40: 41 type=193 (LJ14) 10 13
40: 42 type=193 (LJ14) 10 14
40: 43 type=191 (LJ14) 10 15
40: 44 type=193 (LJ14) 11 13
40: 45 type=193 (LJ14) 11 14
40: 46 type=191 (LJ14) 11 15
40: 47 type=190 (LJ14) 12 19
40: 48 type=190 (LJ14) 12 20
40: 49 type=190 (LJ14) 12 21
40: 50 type=193 (LJ14) 13 16
40: 51 type=193 (LJ14) 13 17
40: 52 type=186 (LJ14) 13 18
40: 53 type=193 (LJ14) 14 16
40: 54 type=193 (LJ14) 14 17
40: 55 type=186 (LJ14) 14 18
40: 56 type=190 (LJ14) 16 19
40: 57 type=190 (LJ14) 16 20
40: 58 type=190 (LJ14) 16 21
40: 59 type=190 (LJ14) 17 19
40: 60 type=190 (LJ14) 17 20
40: 61 type=190 (LJ14) 17 21
40: 62 type=196 (LJ14) 22 27
40: 63 type=197 (LJ14) 22 28
40: 64 type=198 (LJ14) 22 38
40: 65 type=190 (LJ14) 23 25
40: 66 type=195 (LJ14) 23 26
40: 67 type=186 (LJ14) 24 29
40: 68 type=187 (LJ14) 24 30
40: 69 type=187 (LJ14) 24 34
40: 70 type=188 (LJ14) 24 39
40: 71 type=189 (LJ14) 24 40
40: 72 type=190 (LJ14) 25 27
40: 73 type=190 (LJ14) 25 28
40: 74 type=190 (LJ14) 25 38
40: 75 type=191 (LJ14) 26 31
40: 76 type=191 (LJ14) 26 32
40: 77 type=191 (LJ14) 26 33
40: 78 type=191 (LJ14) 26 35
40: 79 type=191 (LJ14) 26 36
40: 80 type=191 (LJ14) 26 37
40: 81 type=190 (LJ14) 26 41
40: 82 type=192 (LJ14) 26 42
40: 83 type=193 (LJ14) 27 29
40: 84 type=191 (LJ14) 27 30
40: 85 type=191 (LJ14) 27 34
40: 86 type=194 (LJ14) 27 39
40: 87 type=186 (LJ14) 27 40
40: 88 type=195 (LJ14) 28 39
40: 89 type=187 (LJ14) 28 40
40: 90 type=193 (LJ14) 29 31
40: 91 type=193 (LJ14) 29 32
40: 92 type=193 (LJ14) 29 33
40: 93 type=193 (LJ14) 29 35
40: 94 type=193 (LJ14) 29 36
40: 95 type=193 (LJ14) 29 37
40: 96 type=196 (LJ14) 29 38
40: 97 type=191 (LJ14) 30 35
40: 98 type=191 (LJ14) 30 36
40: 99 type=191 (LJ14) 30 37
40: 100 type=197 (LJ14) 30 38
40: 101 type=191 (LJ14) 31 34
40: 102 type=191 (LJ14) 32 34
40: 103 type=191 (LJ14) 33 34
40: 104 type=197 (LJ14) 34 38
40: 105 type=196 (LJ14) 38 43
40: 106 type=197 (LJ14) 38 44
40: 107 type=198 (LJ14) 38 58
40: 108 type=190 (LJ14) 39 41
40: 109 type=195 (LJ14) 39 42
40: 110 type=186 (LJ14) 40 45
40: 111 type=186 (LJ14) 40 46
40: 112 type=199 (LJ14) 40 47
40: 113 type=188 (LJ14) 40 59
40: 114 type=189 (LJ14) 40 60
40: 115 type=190 (LJ14) 41 43
40: 116 type=190 (LJ14) 41 44
40: 117 type=190 (LJ14) 41 58
40: 118 type=200 (LJ14) 42 48
40: 119 type=200 (LJ14) 42 50
40: 120 type=190 (LJ14) 42 61
40: 121 type=192 (LJ14) 42 62
40: 122 type=193 (LJ14) 43 45
40: 123 type=193 (LJ14) 43 46
40: 124 type=201 (LJ14) 43 47
40: 125 type=194 (LJ14) 43 59
40: 126 type=186 (LJ14) 43 60
40: 127 type=202 (LJ14) 44 49
40: 128 type=202 (LJ14) 44 51
40: 129 type=200 (LJ14) 44 52
40: 130 type=200 (LJ14) 44 54
40: 131 type=195 (LJ14) 44 59
40: 132 type=187 (LJ14) 44 60
40: 133 type=201 (LJ14) 45 48
40: 134 type=201 (LJ14) 45 50
40: 135 type=196 (LJ14) 45 58
40: 136 type=201 (LJ14) 46 48
40: 137 type=201 (LJ14) 46 50
40: 138 type=196 (LJ14) 46 58
40: 139 type=203 (LJ14) 47 53
40: 140 type=203 (LJ14) 47 55
40: 141 type=204 (LJ14) 47 56
40: 142 type=205 (LJ14) 47 58
40: 143 type=203 (LJ14) 48 51
40: 144 type=204 (LJ14) 48 54
40: 145 type=203 (LJ14) 48 57
40: 146 type=203 (LJ14) 49 50
40: 147 type=206 (LJ14) 49 53
40: 148 type=203 (LJ14) 49 56
40: 149 type=204 (LJ14) 50 52
40: 150 type=203 (LJ14) 50 57
40: 151 type=206 (LJ14) 51 55
40: 152 type=203 (LJ14) 51 56
40: 153 type=203 (LJ14) 52 55
40: 154 type=203 (LJ14) 53 54
40: 155 type=206 (LJ14) 53 57
40: 156 type=206 (LJ14) 55 57
40: 157 type=196 (LJ14) 58 63
40: 158 type=196 (LJ14) 58 64
40: 159 type=198 (LJ14) 58 65
40: 160 type=190 (LJ14) 59 61
40: 161 type=195 (LJ14) 59 62
40: 162 type=188 (LJ14) 60 66
40: 163 type=189 (LJ14) 60 67
40: 164 type=190 (LJ14) 61 63
40: 165 type=190 (LJ14) 61 64
40: 166 type=190 (LJ14) 61 65
40: 167 type=190 (LJ14) 62 68
40: 168 type=192 (LJ14) 62 69
40: 169 type=194 (LJ14) 63 66
40: 170 type=186 (LJ14) 63 67
40: 171 type=194 (LJ14) 64 66
40: 172 type=186 (LJ14) 64 67
40: 173 type=196 (LJ14) 65 70
40: 174 type=197 (LJ14) 65 71
40: 175 type=198 (LJ14) 65 89
40: 176 type=190 (LJ14) 66 68
40: 177 type=195 (LJ14) 66 69
40: 178 type=186 (LJ14) 67 72
40: 179 type=186 (LJ14) 67 73
40: 180 type=187 (LJ14) 67 74
40: 181 type=188 (LJ14) 67 90
40: 182 type=189 (LJ14) 67 91
40: 183 type=190 (LJ14) 68 70
40: 184 type=190 (LJ14) 68 71
40: 185 type=190 (LJ14) 68 89
40: 186 type=191 (LJ14) 69 75
40: 187 type=191 (LJ14) 69 76
40: 188 type=192 (LJ14) 69 77
40: 189 type=190 (LJ14) 69 92
40: 190 type=192 (LJ14) 69 93
40: 191 type=193 (LJ14) 70 72
40: 192 type=193 (LJ14) 70 73
40: 193 type=191 (LJ14) 70 74
40: 194 type=194 (LJ14) 70 90
40: 195 type=186 (LJ14) 70 91
40: 196 type=191 (LJ14) 71 78
40: 197 type=191 (LJ14) 71 79
40: 198 type=187 (LJ14) 71 80
40: 199 type=195 (LJ14) 71 90
40: 200 type=187 (LJ14) 71 91
40: 201 type=193 (LJ14) 72 75
40: 202 type=193 (LJ14) 72 76
40: 203 type=191 (LJ14) 72 77
40: 204 type=196 (LJ14) 72 89
40: 205 type=193 (LJ14) 73 75
40: 206 type=193 (LJ14) 73 76
40: 207 type=191 (LJ14) 73 77
40: 208 type=196 (LJ14) 73 89
40: 209 type=190 (LJ14) 74 81
40: 210 type=207 (LJ14) 74 82
40: 211 type=197 (LJ14) 74 89
40: 212 type=193 (LJ14) 75 78
40: 213 type=193 (LJ14) 75 79
40: 214 type=186 (LJ14) 75 80
40: 215 type=193 (LJ14) 76 78
40: 216 type=193 (LJ14) 76 79
40: 217 type=186 (LJ14) 76 80
40: 218 type=187 (LJ14) 77 83
40: 219 type=187 (LJ14) 77 86
40: 220 type=190 (LJ14) 78 81
40: 221 type=208 (LJ14) 78 82
40: 222 type=190 (LJ14) 79 81
40: 223 type=208 (LJ14) 79 82
40: 224 type=190 (LJ14) 80 84
40: 225 type=190 (LJ14) 80 85
40: 226 type=190 (LJ14) 80 87
40: 227 type=190 (LJ14) 80 88
40: 228 type=190 (LJ14) 81 83
40: 229 type=190 (LJ14) 81 86
40: 230 type=190 (LJ14) 83 87
40: 231 type=190 (LJ14) 83 88
40: 232 type=190 (LJ14) 84 86
40: 233 type=190 (LJ14) 85 86
40: 234 type=196 (LJ14) 89 94
40: 235 type=197 (LJ14) 89 95
40: 236 type=198 (LJ14) 89 100
40: 237 type=190 (LJ14) 90 92
40: 238 type=195 (LJ14) 90 93
40: 239 type=186 (LJ14) 91 96
40: 240 type=186 (LJ14) 91 97
40: 241 type=209 (LJ14) 91 98
40: 242 type=188 (LJ14) 91 101
40: 243 type=189 (LJ14) 91 102
40: 244 type=190 (LJ14) 92 94
40: 245 type=190 (LJ14) 92 95
40: 246 type=190 (LJ14) 92 100
40: 247 type=190 (LJ14) 93 99
40: 248 type=190 (LJ14) 93 103
40: 249 type=192 (LJ14) 93 104
40: 250 type=193 (LJ14) 94 96
40: 251 type=193 (LJ14) 94 97
40: 252 type=210 (LJ14) 94 98
40: 253 type=194 (LJ14) 94 101
40: 254 type=186 (LJ14) 94 102
40: 255 type=195 (LJ14) 95 101
40: 256 type=187 (LJ14) 95 102
40: 257 type=190 (LJ14) 96 99
40: 258 type=196 (LJ14) 96 100
40: 259 type=190 (LJ14) 97 99
40: 260 type=196 (LJ14) 97 100
40: 261 type=211 (LJ14) 98 100
40: 262 type=196 (LJ14) 100 105
40: 263 type=197 (LJ14) 100 106
40: 264 type=198 (LJ14) 100 115
40: 265 type=190 (LJ14) 101 103
40: 266 type=195 (LJ14) 101 104
40: 267 type=186 (LJ14) 102 107
40: 268 type=186 (LJ14) 102 108
40: 269 type=187 (LJ14) 102 109
40: 270 type=188 (LJ14) 102 116
40: 271 type=189 (LJ14) 102 117
40: 272 type=190 (LJ14) 103 105
40: 273 type=190 (LJ14) 103 106
40: 274 type=190 (LJ14) 103 115
40: 275 type=191 (LJ14) 104 110
40: 276 type=191 (LJ14) 104 111
40: 277 type=197 (LJ14) 104 112
40: 278 type=190 (LJ14) 104 118
40: 279 type=192 (LJ14) 104 119
40: 280 type=193 (LJ14) 105 107
40: 281 type=193 (LJ14) 105 108
40: 282 type=191 (LJ14) 105 109
40: 283 type=194 (LJ14) 105 116
40: 284 type=186 (LJ14) 105 117
40: 285 type=195 (LJ14) 106 113
40: 286 type=195 (LJ14) 106 114
40: 287 type=195 (LJ14) 106 116
40: 288 type=187 (LJ14) 106 117
40: 289 type=193 (LJ14) 107 110
40: 290 type=193 (LJ14) 107 111
40: 291 type=196 (LJ14) 107 112
40: 292 type=196 (LJ14) 107 115
40: 293 type=193 (LJ14) 108 110
40: 294 type=193 (LJ14) 108 111
40: 295 type=196 (LJ14) 108 112
40: 296 type=196 (LJ14) 108 115
40: 297 type=197 (LJ14) 109 115
40: 298 type=194 (LJ14) 110 113
40: 299 type=194 (LJ14) 110 114
40: 300 type=194 (LJ14) 111 113
40: 301 type=194 (LJ14) 111 114
40: 302 type=196 (LJ14) 115 120
40: 303 type=197 (LJ14) 115 121
40: 304 type=198 (LJ14) 115 134
40: 305 type=190 (LJ14) 116 118
40: 306 type=195 (LJ14) 116 119
40: 307 type=186 (LJ14) 117 122
40: 308 type=186 (LJ14) 117 123
40: 309 type=187 (LJ14) 117 124
40: 310 type=188 (LJ14) 117 135
40: 311 type=189 (LJ14) 117 136
40: 312 type=190 (LJ14) 118 120
40: 313 type=190 (LJ14) 118 121
40: 314 type=190 (LJ14) 118 134
40: 315 type=191 (LJ14) 119 125
40: 316 type=192 (LJ14) 119 126
40: 317 type=192 (LJ14) 119 130
40: 318 type=190 (LJ14) 119 137
40: 319 type=192 (LJ14) 119 138
40: 320 type=193 (LJ14) 120 122
40: 321 type=193 (LJ14) 120 123
40: 322 type=191 (LJ14) 120 124
40: 323 type=194 (LJ14) 120 135
40: 324 type=186 (LJ14) 120 136
40: 325 type=191 (LJ14) 121 127
40: 326 type=191 (LJ14) 121 128
40: 327 type=191 (LJ14) 121 129
40: 328 type=191 (LJ14) 121 131
40: 329 type=191 (LJ14) 121 132
40: 330 type=191 (LJ14) 121 133
40: 331 type=195 (LJ14) 121 135
40: 332 type=187 (LJ14) 121 136
40: 333 type=193 (LJ14) 122 125
40: 334 type=191 (LJ14) 122 126
40: 335 type=191 (LJ14) 122 130
40: 336 type=196 (LJ14) 122 134
40: 337 type=193 (LJ14) 123 125
40: 338 type=191 (LJ14) 123 126
40: 339 type=191 (LJ14) 123 130
40: 340 type=196 (LJ14) 123 134
40: 341 type=197 (LJ14) 124 134
40: 342 type=193 (LJ14) 125 127
40: 343 type=193 (LJ14) 125 128
40: 344 type=193 (LJ14) 125 129
40: 345 type=193 (LJ14) 125 131
40: 346 type=193 (LJ14) 125 132
40: 347 type=193 (LJ14) 125 133
40: 348 type=191 (LJ14) 126 131
40: 349 type=191 (LJ14) 126 132
40: 350 type=191 (LJ14) 126 133
40: 351 type=191 (LJ14) 127 130
40: 352 type=191 (LJ14) 128 130
40: 353 type=191 (LJ14) 129 130
40: 354 type=196 (LJ14) 134 139
40: 355 type=197 (LJ14) 134 140
40: 356 type=198 (LJ14) 134 144
40: 357 type=190 (LJ14) 135 137
40: 358 type=195 (LJ14) 135 138
40: 359 type=186 (LJ14) 136 141
40: 360 type=186 (LJ14) 136 142
40: 361 type=186 (LJ14) 136 143
40: 362 type=188 (LJ14) 136 145
40: 363 type=189 (LJ14) 136 146
40: 364 type=190 (LJ14) 137 139
40: 365 type=190 (LJ14) 137 140
40: 366 type=190 (LJ14) 137 144
40: 367 type=190 (LJ14) 138 147
40: 368 type=192 (LJ14) 138 148
40: 369 type=193 (LJ14) 139 141
40: 370 type=193 (LJ14) 139 142
40: 371 type=193 (LJ14) 139 143
40: 372 type=194 (LJ14) 139 145
40: 373 type=186 (LJ14) 139 146
40: 374 type=195 (LJ14) 140 145
40: 375 type=187 (LJ14) 140 146
40: 376 type=196 (LJ14) 141 144
40: 377 type=196 (LJ14) 142 144
40: 378 type=196 (LJ14) 143 144
40: 379 type=196 (LJ14) 144 149
40: 380 type=197 (LJ14) 144 150
40: 381 type=198 (LJ14) 144 154
40: 382 type=190 (LJ14) 145 147
40: 383 type=195 (LJ14) 145 148
40: 384 type=186 (LJ14) 146 151
40: 385 type=186 (LJ14) 146 152
40: 386 type=186 (LJ14) 146 153
40: 387 type=188 (LJ14) 146 155
40: 388 type=190 (LJ14) 147 149
40: 389 type=190 (LJ14) 147 150
40: 390 type=190 (LJ14) 147 154
40: 391 type=193 (LJ14) 149 151
40: 392 type=193 (LJ14) 149 152
40: 393 type=193 (LJ14) 149 153
40: 394 type=194 (LJ14) 149 155
40: 395 type=195 (LJ14) 150 155
40: 396 type=196 (LJ14) 151 154
40: 397 type=196 (LJ14) 152 154
40: 398 type=196 (LJ14) 153 154
40: Coulomb-14:
40: nr: 0
40: LJC-14 q:
40: nr: 0
40: LJC Pairs NB:
40: nr: 0
40: LJ (SR):
40: nr: 0
40: Buck.ham (SR):
40: nr: 0
40: LJ (unused):
40: nr: 0
40: B.ham (unused):
40: nr: 0
40: Disper. corr.:
40: nr: 0
40: Coulomb (SR):
40: nr: 0
40: Coul (unused):
40: nr: 0
40: RF excl.:
40: nr: 0
40: Coul. recip.:
40: nr: 0
40: LJ recip.:
40: nr: 0
40: DPD:
40: nr: 0
40: Polarization:
40: nr: 0
40: Water Pol.:
40: nr: 0
40: Thole Pol.:
40: nr: 0
40: Anharm. Pol.:
40: nr: 0
40: Position Rest.:
40: nr: 0
40: Flat-bottom posres:
40: nr: 0
40: Dis. Rest.:
40: nr: 0
40: D.R.Viol. (nm):
40: nr: 0
40: Orient. Rest.:
40: nr: 0
40: Ori. R. RMSD:
40: nr: 0
40: Angle Rest.:
40: nr: 0
40: Angle Rest. Z:
40: nr: 0
40: Dih. Rest.:
40: nr: 0
40: Dih. Rest. Viol.:
40: nr: 0
40: Constraint:
40: nr: 0
40: Constr. No Conn.:
40: nr: 0
40: Settle:
40: nr: 0
40: Virtual site 2:
40: nr: 0
40: Virtual site 2fd:
40: nr: 0
40: Virtual site 3:
40: nr: 0
40: Virtual site 3fd:
40: nr: 0
40: Virtual site 3fad:
40: nr: 0
40: Virtual site 3out:
40: nr: 0
40: Virtual site 4fd:
40: nr: 0
40: Virtual site 4fdn:
40: nr: 0
40: Virtual site N:
40: nr: 0
40: COM Pull En.:
40: nr: 0
40: Density fitting:
40: nr: 0
40: Quantum En.:
40: nr: 0
40: Potential:
40: nr: 0
40: Kinetic En.:
40: nr: 0
40: Total Energy:
40: nr: 0
40: Conserved En.:
40: nr: 0
40: Temperature:
40: nr: 0
40: Vir. Temp. (not used):
40: nr: 0
40: Pres. DC:
40: nr: 0
40: Pressure:
40: nr: 0
40: dH/dl constr.:
40: nr: 0
40: dVremain/dl:
40: nr: 0
40: dEkin/dl:
40: nr: 0
40: dVcoul/dl:
40: nr: 0
40: dVvdw/dl:
40: nr: 0
40: dVbonded/dl:
40: nr: 0
40: dVrestraint/dl:
40: nr: 0
40: dVtemperature/dl:
40: nr: 0
40: grp[T-Coupling ] nr=1, name=[ rest]
40: grp[Energy Mon. ] nr=1, name=[ rest]
40: grp[Acceleration] nr=1, name=[ rest]
40: grp[Freeze ] nr=1, name=[ rest]
40: grp[User1 ] nr=1, name=[ rest]
40: grp[User2 ] nr=1, name=[ rest]
40: grp[VCM ] nr=1, name=[ rest]
40: grp[Compressed X] nr=1, name=[ rest]
40: grp[Or. Res. Fit] nr=1, name=[ rest]
40: grp[QMMM ] nr=1, name=[ rest]
40: grpname (11):
40: grpname[0]={name="System"}
40: grpname[1]={name="Protein"}
40: grpname[2]={name="Protein-H"}
40: grpname[3]={name="C-alpha"}
40: grpname[4]={name="Backbone"}
40: grpname[5]={name="MainChain"}
40: grpname[6]={name="MainChain+Cb"}
40: grpname[7]={name="MainChain+H"}
40: grpname[8]={name="SideChain"}
40: grpname[9]={name="SideChain-H"}
40: grpname[10]={name="rest"}
40: groups T-Cou Energ Accel Freez User1 User2 VCM Compr Or. R QMMM
40: allocated 0 0 0 0 0 0 0 0 0 0
40: groupnr[ *] = 0 0 0 0 0 0 0 0 0 0
40: box (3x3):
40: box[ 0]={ 5.90620e+00, 0.00000e+00, 0.00000e+00}
40: box[ 1]={ 0.00000e+00, 6.84510e+00, 0.00000e+00}
40: box[ 2]={ 0.00000e+00, 0.00000e+00, 3.05170e+00}
40: box_rel (3x3):
40: box_rel[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: box_rel[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: box_rel[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: boxv (3x3):
40: boxv[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: boxv[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: boxv[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: pres_prev (3x3):
40: pres_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: pres_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: pres_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: svir_prev (3x3):
40: svir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: svir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: svir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: fvir_prev (3x3):
40: fvir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: fvir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: fvir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: nosehoover_xi: not available
40: x (156x3):
40: x[ 0]={ 3.53600e+00, 2.23400e+00, -1.19800e+00}
40: x[ 1]={ 3.61200e+00, 2.28800e+00, -1.23600e+00}
40: x[ 2]={ 3.47000e+00, 2.21400e+00, -1.27000e+00}
40: x[ 3]={ 3.49200e+00, 2.28600e+00, -1.12500e+00}
40: x[ 4]={ 3.58900e+00, 2.10700e+00, -1.14300e+00}
40: x[ 5]={ 3.63300e+00, 2.05500e+00, -1.21600e+00}
40: x[ 6]={ 3.68700e+00, 2.14400e+00, -1.03100e+00}
40: x[ 7]={ 3.76300e+00, 2.19500e+00, -1.07000e+00}
40: x[ 8]={ 3.63900e+00, 2.20100e+00, -9.64000e-01}
40: x[ 9]={ 3.74500e+00, 2.02500e+00, -9.56000e-01}
40: x[ 10]={ 3.67600e+00, 1.98900e+00, -8.94000e-01}
40: x[ 11]={ 3.77000e+00, 1.95400e+00, -1.02300e+00}
40: x[ 12]={ 3.86900e+00, 2.06500e+00, -8.77000e-01}
40: x[ 13]={ 3.94500e+00, 2.08300e+00, -9.40000e-01}
40: x[ 14]={ 3.84900e+00, 2.14700e+00, -8.24000e-01}
40: x[ 15]={ 3.90600e+00, 1.95100e+00, -7.84000e-01}
40: x[ 16]={ 3.84100e+00, 1.94600e+00, -7.08000e-01}
40: x[ 17]={ 3.90600e+00, 1.86400e+00, -8.33000e-01}
40: x[ 18]={ 4.04200e+00, 1.97700e+00, -7.30000e-01}
40: x[ 19]={ 4.06900e+00, 1.90300e+00, -6.68000e-01}
40: x[ 20]={ 4.10800e+00, 1.98200e+00, -8.06000e-01}
40: x[ 21]={ 4.04200e+00, 2.06400e+00, -6.80000e-01}
40: x[ 22]={ 3.47400e+00, 2.02600e+00, -1.08400e+00}
40: x[ 23]={ 3.39500e+00, 2.08100e+00, -1.00800e+00}
40: x[ 24]={ 3.47400e+00, 1.89600e+00, -1.10400e+00}
40: x[ 25]={ 3.53600e+00, 1.86000e+00, -1.17400e+00}
40: x[ 26]={ 3.39000e+00, 1.80000e+00, -1.03300e+00}
40: x[ 27]={ 3.31700e+00, 1.85200e+00, -9.90000e-01}
40: x[ 28]={ 3.31400e+00, 1.70300e+00, -1.12300e+00}
40: x[ 29]={ 3.38600e+00, 1.65200e+00, -1.17000e+00}
40: x[ 30]={ 3.22500e+00, 1.60800e+00, -1.04300e+00}
40: x[ 31]={ 3.17700e+00, 1.54700e+00, -1.10600e+00}
40: x[ 32]={ 3.28200e+00, 1.55500e+00, -9.81000e-01}
40: x[ 33]={ 3.15800e+00, 1.66100e+00, -9.91000e-01}
40: x[ 34]={ 3.22900e+00, 1.77100e+00, -1.22900e+00}
40: x[ 35]={ 3.18300e+00, 1.70200e+00, -1.28400e+00}
40: x[ 36]={ 3.16200e+00, 1.83000e+00, -1.18500e+00}
40: x[ 37]={ 3.28800e+00, 1.82700e+00, -1.28800e+00}
40: x[ 38]={ 3.48000e+00, 1.73100e+00, -9.29000e-01}
40: x[ 39]={ 3.57600e+00, 1.66100e+00, -9.66000e-01}
40: x[ 40]={ 3.44900e+00, 1.75500e+00, -8.04000e-01}
40: x[ 41]={ 3.37500e+00, 1.81900e+00, -7.84000e-01}
40: x[ 42]={ 3.51900e+00, 1.69000e+00, -6.92000e-01}
40: x[ 43]={ 3.61500e+00, 1.69700e+00, -7.17000e-01}
40: x[ 44]={ 3.49700e+00, 1.76300e+00, -5.59000e-01}
40: x[ 45]={ 3.40500e+00, 1.80200e+00, -5.58000e-01}
40: x[ 46]={ 3.50600e+00, 1.69800e+00, -4.84000e-01}
40: x[ 47]={ 3.59400e+00, 1.87400e+00, -5.38000e-01}
40: x[ 48]={ 3.56700e+00, 2.00500e+00, -5.80000e-01}
40: x[ 49]={ 3.48100e+00, 2.02500e+00, -6.27000e-01}
40: x[ 50]={ 3.70000e+00, 1.85600e+00, -4.47000e-01}
40: x[ 51]={ 3.71300e+00, 1.76600e+00, -4.05000e-01}
40: x[ 52]={ 3.65800e+00, 2.10800e+00, -5.57000e-01}
40: x[ 53]={ 3.64800e+00, 2.19500e+00, -6.04000e-01}
40: x[ 54]={ 3.78700e+00, 1.95900e+00, -4.16000e-01}
40: x[ 55]={ 3.86600e+00, 1.94200e+00, -3.57000e-01}
40: x[ 56]={ 3.76400e+00, 2.08700e+00, -4.67000e-01}
40: x[ 57]={ 3.82200e+00, 2.16400e+00, -4.39000e-01}
40: x[ 58]={ 3.47400e+00, 1.54400e+00, -6.77000e-01}
40: x[ 59]={ 3.35200e+00, 1.51600e+00, -6.86000e-01}
40: x[ 60]={ 3.57200e+00, 1.46400e+00, -6.33000e-01}
40: x[ 61]={ 3.66700e+00, 1.49500e+00, -6.32000e-01}
40: x[ 62]={ 3.53700e+00, 1.32800e+00, -5.87000e-01}
40: x[ 63]={ 3.46200e+00, 1.29200e+00, -6.43000e-01}
40: x[ 64]={ 3.61600e+00, 1.26800e+00, -5.94000e-01}
40: x[ 65]={ 3.49200e+00, 1.34200e+00, -4.42000e-01}
40: x[ 66]={ 3.53000e+00, 1.44000e+00, -3.78000e-01}
40: x[ 67]={ 3.40500e+00, 1.25400e+00, -3.97000e-01}
40: x[ 68]={ 3.37100e+00, 1.18400e+00, -4.60000e-01}
40: x[ 69]={ 3.35600e+00, 1.25400e+00, -2.59000e-01}
40: x[ 70]={ 3.29800e+00, 1.33400e+00, -2.52000e-01}
40: x[ 71]={ 3.27600e+00, 1.12600e+00, -2.33000e-01}
40: x[ 72]={ 3.20000e+00, 1.12200e+00, -2.97000e-01}
40: x[ 73]={ 3.33600e+00, 1.04700e+00, -2.47000e-01}
40: x[ 74]={ 3.22100e+00, 1.12000e+00, -9.20000e-02}
40: x[ 75]={ 3.29700e+00, 1.11700e+00, -2.70000e-02}
40: x[ 76]={ 3.16500e+00, 1.20100e+00, -7.50000e-02}
40: x[ 77]={ 3.13800e+00, 1.00000e+00, -7.20000e-02}
40: x[ 78]={ 3.10400e+00, 9.99000e-01, 2.20000e-02}
40: x[ 79]={ 3.06000e+00, 1.00500e+00, -1.35000e-01}
40: x[ 80]={ 3.20600e+00, 8.75000e-01, -9.60000e-02}
40: x[ 81]={ 3.20200e+00, 8.40000e-01, -1.89000e-01}
40: x[ 82]={ 3.27300e+00, 8.01000e-01, -1.00000e-02}
40: x[ 83]={ 3.28400e+00, 8.33000e-01, 1.19000e-01}
40: x[ 84]={ 3.23900e+00, 9.16000e-01, 1.53000e-01}
40: x[ 85]={ 3.33600e+00, 7.75000e-01, 1.81000e-01}
40: x[ 86]={ 3.32500e+00, 6.84000e-01, -5.30000e-02}
40: x[ 87]={ 3.31100e+00, 6.55000e-01, -1.47000e-01}
40: x[ 88]={ 3.37600e+00, 6.26000e-01, 1.00000e-02}
40: x[ 89]={ 3.46700e+00, 1.27300e+00, -1.56000e-01}
40: x[ 90]={ 3.46700e+00, 1.36500e+00, -7.00000e-02}
40: x[ 91]={ 3.56700e+00, 1.18500e+00, -1.61000e-01}
40: x[ 92]={ 3.56700e+00, 1.11600e+00, -2.33000e-01}
40: x[ 93]={ 3.67800e+00, 1.18700e+00, -6.50000e-02}
40: x[ 94]={ 3.63100e+00, 1.20200e+00, 2.20000e-02}
40: x[ 95]={ 3.74900e+00, 1.05300e+00, -6.20000e-02}
40: x[ 96]={ 3.77000e+00, 1.03400e+00, -1.58000e-01}
40: x[ 97]={ 3.83400e+00, 1.07200e+00, -1.30000e-02}
40: x[ 98]={ 3.65400e+00, 9.20000e-01, 1.40000e-02}
40: x[ 99]={ 3.70750e+00, 8.35500e-01, 1.20000e-02}
40: x[ 100]={ 3.77500e+00, 1.30500e+00, -7.80000e-02}
40: x[ 101]={ 3.81500e+00, 1.36100e+00, 2.60000e-02}
40: x[ 102]={ 3.78600e+00, 1.34800e+00, -2.02000e-01}
40: x[ 103]={ 3.74000e+00, 1.30000e+00, -2.76000e-01}
40: x[ 104]={ 3.86800e+00, 1.46900e+00, -2.31000e-01}
40: x[ 105]={ 3.96000e+00, 1.45500e+00, -1.93000e-01}
40: x[ 106]={ 3.87800e+00, 1.48500e+00, -3.82000e-01}
40: x[ 107]={ 3.92300e+00, 1.40200e+00, -4.17000e-01}
40: x[ 108]={ 3.78500e+00, 1.48900e+00, -4.17000e-01}
40: x[ 109]={ 3.95400e+00, 1.60500e+00, -4.38000e-01}
40: x[ 110]={ 3.91300e+00, 1.68700e+00, -3.99000e-01}
40: x[ 111]={ 4.04900e+00, 1.59800e+00, -4.07000e-01}
40: x[ 112]={ 3.95800e+00, 1.62400e+00, -5.87000e-01}
40: x[ 113]={ 3.86700e+00, 1.56400e+00, -6.49000e-01}
40: x[ 114]={ 4.04200e+00, 1.69500e+00, -6.38000e-01}
40: x[ 115]={ 3.80500e+00, 1.59300e+00, -1.66000e-01}
40: x[ 116]={ 3.87400e+00, 1.67300e+00, -1.01000e-01}
40: x[ 117]={ 3.67400e+00, 1.60500e+00, -1.82000e-01}
40: x[ 118]={ 3.62600e+00, 1.53500e+00, -2.35000e-01}
40: x[ 119]={ 3.59600e+00, 1.71600e+00, -1.25000e-01}
40: x[ 120]={ 3.64000e+00, 1.80100e+00, -1.56000e-01}
40: x[ 121]={ 3.45300e+00, 1.71700e+00, -1.81000e-01}
40: x[ 122]={ 3.45700e+00, 1.72200e+00, -2.81000e-01}
40: x[ 123]={ 3.40600e+00, 1.63300e+00, -1.53000e-01}
40: x[ 124]={ 3.37200e+00, 1.83500e+00, -1.31000e-01}
40: x[ 125]={ 3.37800e+00, 1.84200e+00, -3.10000e-02}
40: x[ 126]={ 3.43000e+00, 1.96600e+00, -1.84000e-01}
40: x[ 127]={ 3.37600e+00, 2.04300e+00, -1.50000e-01}
40: x[ 128]={ 3.52400e+00, 1.97500e+00, -1.53000e-01}
40: x[ 129]={ 3.42700e+00, 1.96500e+00, -2.84000e-01}
40: x[ 130]={ 3.22500e+00, 1.81400e+00, -1.60000e-01}
40: x[ 131]={ 3.17200e+00, 1.89300e+00, -1.26000e-01}
40: x[ 132]={ 3.21100e+00, 1.80500e+00, -2.58000e-01}
40: x[ 133]={ 3.19300e+00, 1.73100e+00, -1.14000e-01}
40: x[ 134]={ 3.60500e+00, 1.71300e+00, 2.70000e-02}
40: x[ 135]={ 3.61600e+00, 1.81700e+00, 9.20000e-02}
40: x[ 136]={ 3.57500e+00, 1.59800e+00, 8.30000e-02}
40: x[ 137]={ 3.54600e+00, 1.52200e+00, 2.40000e-02}
40: x[ 138]={ 3.58400e+00, 1.57600e+00, 2.28000e-01}
40: x[ 139]={ 3.50800e+00, 1.62600e+00, 2.69000e-01}
40: x[ 140]={ 3.56600e+00, 1.42900e+00, 2.62000e-01}
40: x[ 141]={ 3.57200e+00, 1.41600e+00, 3.61000e-01}
40: x[ 142]={ 3.47600e+00, 1.39800e+00, 2.30000e-01}
40: x[ 143]={ 3.63700e+00, 1.37500e+00, 2.18000e-01}
40: x[ 144]={ 3.71400e+00, 1.63100e+00, 2.84000e-01}
40: x[ 145]={ 3.71500e+00, 1.69800e+00, 3.90000e-01}
40: x[ 146]={ 3.82700e+00, 1.59800e+00, 2.20000e-01}
40: x[ 147]={ 3.82000e+00, 1.53900e+00, 1.40000e-01}
40: x[ 148]={ 3.96100e+00, 1.64300e+00, 2.62000e-01}
40: x[ 149]={ 3.96900e+00, 1.61900e+00, 3.58000e-01}
40: x[ 150]={ 4.07100e+00, 1.57100e+00, 1.84000e-01}
40: x[ 151]={ 4.16000e+00, 1.60300e+00, 2.15000e-01}
40: x[ 152]={ 4.06400e+00, 1.47200e+00, 2.01000e-01}
40: x[ 153]={ 4.06000e+00, 1.58900e+00, 8.60000e-02}
40: x[ 154]={ 3.97400e+00, 1.79400e+00, 2.46000e-01}
40: x[ 155]={ 4.01900e+00, 1.85000e+00, 3.47000e-01}
40: v (156x3):
40: v[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 3]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 4]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 5]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 6]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 7]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 8]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 9]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 10]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 11]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 12]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 13]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 14]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 15]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 16]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 17]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 18]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 19]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 20]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 21]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 22]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 23]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 24]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 25]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 26]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 27]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 28]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 29]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 30]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 31]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 32]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 33]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 34]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 35]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 36]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 37]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 38]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 39]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 40]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 41]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 42]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 43]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 44]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 45]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 46]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 47]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 48]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 49]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 50]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 51]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 52]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 53]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 54]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 55]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 56]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 57]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 58]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 59]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 60]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 61]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 62]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 63]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 64]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 65]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 66]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 67]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 68]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 69]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 70]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 71]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 72]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 73]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 74]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 75]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 76]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 77]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 78]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 79]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 80]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 81]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 82]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 83]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 84]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 85]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 86]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 87]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 88]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 89]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 90]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 91]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 92]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 93]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 94]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 95]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 96]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 97]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 98]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 99]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 100]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 101]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 102]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 103]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 104]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 105]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 106]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 107]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 108]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 109]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 110]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 111]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 112]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 113]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 114]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 115]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 116]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 117]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 118]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 119]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 120]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 121]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 122]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 123]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 124]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 125]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 126]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 127]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 128]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 129]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 130]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 131]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 132]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 133]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 134]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 135]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 136]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 137]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 138]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 139]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 140]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 141]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 142]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 143]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 144]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 145]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 146]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 147]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 148]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 149]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 150]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 151]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 152]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 153]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 154]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: v[ 155]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
40: Group statistics
40: T-Coupling : 156 (total 156 atoms)
40: Energy Mon. : 156 (total 156 atoms)
40: Acceleration: 156 (total 156 atoms)
40: Freeze : 156 (total 156 atoms)
40: User1 : 156 (total 156 atoms)
40: User2 : 156 (total 156 atoms)
40: VCM : 156 (total 156 atoms)
40: Compressed X: 156 (total 156 atoms)
40: Or. Res. Fit: 156 (total 156 atoms)
40: QMMM : 156 (total 156 atoms)
40: [ OK ] DumpTest.WorksWithTpr (40 ms)
40: [ RUN ] DumpTest.WorksWithTprAndMdpWriting
40: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
40: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
40: [ OK ] DumpTest.WorksWithTprAndMdpWriting (8 ms)
40: [----------] 2 tests from DumpTest (58 ms total)
40:
40: [----------] 4 tests from ReportMethodsTest
40:
40: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]:
40: For a correct single-point energy evaluation with nsteps = 0, use
40: continuation = yes to avoid constraining the input coordinates.
40:
40: Setting the LD random seed to -1471665024
40: Generated 330891 of the 330891 non-bonded parameter combinations
40: Generating 1-4 interactions: fudge = 0.5
40: Generated 330891 of the 330891 1-4 parameter combinations
40: Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
40:
40: NOTE 2 [file lysozyme.top, line 1465]:
40: System has non-zero total charge: 2.000000
40: Total charge should normally be an integer. See
40: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
40: for discussion on how close it should be to an integer.
40:
40:
40:
40: Number of degrees of freedom in T-Coupling group rest is 465.00
40:
40: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]:
40: NVE simulation with an initial temperature of zero: will use a Verlet
40: buffer of 10%. Check your energy drift!
40:
40:
40: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]:
40: You are using a plain Coulomb cut-off, which might produce artifacts.
40: You might want to consider using PME electrostatics.
40:
40:
40:
40: There were 4 notes
40: Analysing residue names:
40: There are: 10 Protein residues
40: Analysing Protein...
40: This run will generate roughly 0 Mb of data
40: [ RUN ] ReportMethodsTest.WritesCorrectHeadersFormated
40: [ OK ] ReportMethodsTest.WritesCorrectHeadersFormated (0 ms)
40: [ RUN ] ReportMethodsTest.WritesCorrectHeadersUnformatted
40: [ OK ] ReportMethodsTest.WritesCorrectHeadersUnformatted (0 ms)
40: [ RUN ] ReportMethodsTest.WritesCorrectInformation
40: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
40: [ OK ] ReportMethodsTest.WritesCorrectInformation (5 ms)
40: [ RUN ] ReportMethodsTest.ToolEndToEndTest
40: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
40: section: Methods
40: subsection: Simulation system
40: A system of 1 molecules (156 atoms) was simulated.
40:
40: subsection: Simulation settings
40: A total of 0 ns were simulated with a time step of 1 fs.
40: Neighbor searching was performed every 10 steps.
40: The Cut-off algorithm was used for electrostatic interactions.
40: with a cut-off of 1 nm.
40: A single cut-off of 1.1 nm was used for Van der Waals interactions.
40: [ OK ] ReportMethodsTest.ToolEndToEndTest (5 ms)
40: [----------] 4 tests from ReportMethodsTest (10 ms total)
40:
40: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset
40: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/0
40: Will write tng: Trajectory file (tng format)
40: Group 0 ( System) has 6 elements
40: Group 1 (FirstWaterMolecule) has 3 elements
40: Group 2 (SecondWaterMolecule) has 3 elements
40: Select a group: trr version: GMX_trn_file (single precision)
40:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
40:
40: Note that major changes are planned in future for trjconv, to improve usability and utility.
40: Select group for output
40: Selected 2: 'SecondWaterMolecule'
40: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/0 (16 ms)
40: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/1
40: Will write tng: Trajectory file (tng format)
40: Group 0 ( System) has 6 elements
40: Group 1 (FirstWaterMolecule) has 3 elements
40: Group 2 (SecondWaterMolecule) has 3 elements
40: Select a group:
Reading frame 0 time 0.000
40: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm)
40: -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
40:
40: Note that major changes are planned in future for trjconv, to improve usability and utility.
40: Select group for output
40: Selected 2: 'SecondWaterMolecule'
40: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/1 (16 ms)
40: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/2
40: Will write tng: Trajectory file (tng format)
40: Group 0 ( System) has 6 elements
40: Group 1 (FirstWaterMolecule) has 3 elements
40: Group 2 (SecondWaterMolecule) has 3 elements
40: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
40:
40: Note that major changes are planned in future for trjconv, to improve usability and utility.
40: Select group for output
40: Selected 2: 'SecondWaterMolecule'
40: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/2 (14 ms)
40: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/3
40: Will write tng: Trajectory file (tng format)
40: Group 0 ( System) has 6 elements
40: Group 1 (FirstWaterMolecule) has 3 elements
40: Group 2 (SecondWaterMolecule) has 3 elements
40: Select a group: Reading frames from gro file '', 6 atoms.
40:
Reading frame 0 time 0.000
40: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm)
40: -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
40:
40: Note that major changes are planned in future for trjconv, to improve usability and utility.
40: Select group for output
40: Selected 2: 'SecondWaterMolecule'
40: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/3 (15 ms)
40: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/4
40: Will write tng: Trajectory file (tng format)
40: Group 0 ( System) has 6 elements
40: Group 1 (FirstWaterMolecule) has 3 elements
40: Group 2 (SecondWaterMolecule) has 3 elements
40: Select a group: Reading frames from pdb file
Reading frame 0 time 0.000
40: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm)
40: -> frame 0 time 0.000
't= 0.00000', 6 atoms
40:
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
40:
40: Note that major changes are planned in future for trjconv, to improve usability and utility.
40: Select group for output
40: Selected 2: 'SecondWaterMolecule'
40: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/4 (14 ms)
40: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/5
40: Will write tng: Trajectory file (tng format)
40: Group 0 ( System) has 6 elements
40: Group 1 (FirstWaterMolecule) has 3 elements
40: Group 2 (SecondWaterMolecule) has 3 elements
40: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
40:
40: Note that major changes are planned in future for trjconv, to improve usability and utility.
40: Select group for output
40: Selected 2: 'SecondWaterMolecule'
40: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/5 (15 ms)
40: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset (90 ms total)
40:
40: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile
40: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/0
40: Will write trr: Trajectory in portable xdr format
40: Group 0 ( System) has 6 elements
40: Group 1 (FirstWaterMolecule) has 3 elements
40: Group 2 (SecondWaterMolecule) has 3 elements
40: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
40:
40: Note that major changes are planned in future for trjconv, to improve usability and utility.
40: Select group for output
40: Selected 2: 'SecondWaterMolecule'
40: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/0 (4 ms)
40: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/1
40: Will write trr: Trajectory in portable xdr format
40: Group 0 ( System) has 6 elements
40: Group 1 (FirstWaterMolecule) has 3 elements
40: Group 2 (SecondWaterMolecule) has 3 elements
40: Select a group:
Reading frame 0 time 0.000
40: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm)
40: -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
40:
40: Note that major changes are planned in future for trjconv, to improve usability and utility.
40: Select group for output
40: Selected 2: 'SecondWaterMolecule'
40: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/1 (5 ms)
40: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/2
40: Will write trr: Trajectory in portable xdr format
40: Group 0 ( System) has 6 elements
40: Group 1 (FirstWaterMolecule) has 3 elements
40: Group 2 (SecondWaterMolecule) has 3 elements
40: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
40:
40: Note that major changes are planned in future for trjconv, to improve usability and utility.
40: Select group for output
40: Selected 2: 'SecondWaterMolecule'
40: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/2 (3 ms)
40: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/3
40: Will write trr: Trajectory in portable xdr format
40: Group 0 ( System) has 6 elements
40: Group 1 (FirstWaterMolecule) has 3 elements
40: Group 2 (SecondWaterMolecule) has 3 elements
40: Select a group: Reading frames from gro file '', 6 atoms.
40:
Reading frame 0 time 0.000
40: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm)
40: -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
40:
40: Note that major changes are planned in future for trjconv, to improve usability and utility.
40: Select group for output
40: Selected 2: 'SecondWaterMolecule'
40: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/3 (5 ms)
40: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/4
40: Will write trr: Trajectory in portable xdr format
40: Group 0 ( System) has 6 elements
40: Group 1 (FirstWaterMolecule) has 3 elements
40: Group 2 (SecondWaterMolecule) has 3 elements
40: Select a group: Reading frames from pdb file
Reading frame 0 time 0.000
40: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm)
40: -> frame 0 time 0.000
't= 0.00000', 6 atoms
40:
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
40:
40: Note that major changes are planned in future for trjconv, to improve usability and utility.
40: Select group for output
40: Selected 2: 'SecondWaterMolecule'
40: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/4 (3 ms)
40: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/5
40: Will write trr: Trajectory in portable xdr format
40: Group 0 ( System) has 6 elements
40: Group 1 (FirstWaterMolecule) has 3 elements
40: Group 2 (SecondWaterMolecule) has 3 elements
40: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
40:
40: Note that major changes are planned in future for trjconv, to improve usability and utility.
40: Select group for output
40: Selected 2: 'SecondWaterMolecule'
40: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/5 (4 ms)
40: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile (25 ms total)
40:
40: [----------] Global test environment tear-down
40: [==========] 18 tests from 4 test cases ran. (9162 ms total)
40: [ PASSED ] 18 tests.
40/52 Test #40: ToolUnitTests ....................... Passed 9.23 sec
test 41
Start 41: FileIOTests
41: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/fileio-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/FileIOTests.xml"
41: Test timeout computed to be: 30
41: [==========] Running 33 tests from 8 test cases.
41: [----------] Global test environment set-up.
41: [----------] 2 tests from FileMD5Test
41: [ RUN ] FileMD5Test.CanComputeMD5
41: [ OK ] FileMD5Test.CanComputeMD5 (4 ms)
41: [ RUN ] FileMD5Test.ReturnsErrorIfFileModeIsWrong
41: [ OK ] FileMD5Test.ReturnsErrorIfFileModeIsWrong (1 ms)
41: [----------] 2 tests from FileMD5Test (7 ms total)
41:
41: [----------] 3 tests from MrcSerializer
41: [ RUN ] MrcSerializer.DefaultHeaderValuesAreSet
41: [ OK ] MrcSerializer.DefaultHeaderValuesAreSet (0 ms)
41: [ RUN ] MrcSerializer.DefaultHeaderHasRightSerialSize
41: [ OK ] MrcSerializer.DefaultHeaderHasRightSerialSize (0 ms)
41: [ RUN ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip
41: [ OK ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip (4 ms)
41: [----------] 3 tests from MrcSerializer (6 ms total)
41:
41: [----------] 4 tests from MrcDensityMap
41: [ RUN ] MrcDensityMap.RoundTripIsIdempotent
41: [ OK ] MrcDensityMap.RoundTripIsIdempotent (5 ms)
41: [ RUN ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent
41: [ OK ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent (1 ms)
41: [ RUN ] MrcDensityMap.ReadsCoordinateTransformationFromFile
41: [ OK ] MrcDensityMap.ReadsCoordinateTransformationFromFile (1 ms)
41: [ RUN ] MrcDensityMap.ReadsDensityDataFromFile
41: [ OK ] MrcDensityMap.ReadsDensityDataFromFile (26 ms)
41: [----------] 4 tests from MrcDensityMap (36 ms total)
41:
41: [----------] 8 tests from MrcDensityMapHeaderTest
41: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader
41: [ OK ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader (0 ms)
41: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsCorrect
41: [ OK ] MrcDensityMapHeaderTest.DataSizeIsCorrect (0 ms)
41: [ RUN ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid
41: [ OK ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid (1 ms)
41: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven
41: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven (0 ms)
41: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined
41: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined (0 ms)
41: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues
41: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues (0 ms)
41: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectExtents
41: [ OK ] MrcDensityMapHeaderTest.GetsCorrectExtents (0 ms)
41: [ RUN ] MrcDensityMapHeaderTest.IsSane
41: [ OK ] MrcDensityMapHeaderTest.IsSane (0 ms)
41: [----------] 8 tests from MrcDensityMapHeaderTest (5 ms total)
41:
41: [----------] 9 tests from ReadTest
41: [ RUN ] ReadTest.get_eint_ReadsInteger
41: [ OK ] ReadTest.get_eint_ReadsInteger (0 ms)
41: [ RUN ] ReadTest.get_eint_WarnsAboutFloat
41:
41: ERROR 1 [file unknown, line 0]:
41: Right hand side '0.8' for parameter 'test' in parameter file is not an
41: integer value
41:
41:
41: [ OK ] ReadTest.get_eint_WarnsAboutFloat (0 ms)
41: [ RUN ] ReadTest.get_eint_WarnsAboutString
41:
41: ERROR 1 [file unknown, line 0]:
41: Right hand side 'hello' for parameter 'test' in parameter file is not an
41: integer value
41:
41:
41: [ OK ] ReadTest.get_eint_WarnsAboutString (0 ms)
41: [ RUN ] ReadTest.get_eint64_ReadsInteger
41: [ OK ] ReadTest.get_eint64_ReadsInteger (0 ms)
41: [ RUN ] ReadTest.get_eint64_WarnsAboutFloat
41:
41: ERROR 1 [file unknown, line 0]:
41: Right hand side '0.8' for parameter 'test' in parameter file is not an
41: integer value
41:
41:
41: [ OK ] ReadTest.get_eint64_WarnsAboutFloat (1 ms)
41: [ RUN ] ReadTest.get_eint64_WarnsAboutString
41:
41: ERROR 1 [file unknown, line 0]:
41: Right hand side 'hello' for parameter 'test' in parameter file is not an
41: integer value
41:
41:
41: [ OK ] ReadTest.get_eint64_WarnsAboutString (1 ms)
41: [ RUN ] ReadTest.get_ereal_ReadsInteger
41: [ OK ] ReadTest.get_ereal_ReadsInteger (0 ms)
41: [ RUN ] ReadTest.get_ereal_ReadsFloat
41: [ OK ] ReadTest.get_ereal_ReadsFloat (0 ms)
41: [ RUN ] ReadTest.get_ereal_WarnsAboutString
41:
41: ERROR 1 [file unknown, line 0]:
41: Right hand side 'hello' for parameter 'test' in parameter file is not a
41: real value
41:
41:
41: [ OK ] ReadTest.get_ereal_WarnsAboutString (0 ms)
41: [----------] 9 tests from ReadTest (7 ms total)
41:
41: [----------] 1 test from FileIOXdrSerializerTest
41: [ RUN ] FileIOXdrSerializerTest.SizeIsCorrect
41: [ OK ] FileIOXdrSerializerTest.SizeIsCorrect (2 ms)
41: [----------] 1 test from FileIOXdrSerializerTest (2 ms total)
41:
41: [----------] 2 tests from TngTest
41: [ RUN ] TngTest.CanOpenTngFile
41: TNG library: Cannot open file spc2-traj.tng. /<<PKGBUILDDIR>>/src/external/tng_io/src/lib/tng_io.c: 890
41: TNG library: Cannot open file spc2-traj.tng. /<<PKGBUILDDIR>>/src/external/tng_io/src/lib/tng_io.c: 890
41: [ OK ] TngTest.CanOpenTngFile (1 ms)
41: [ RUN ] TngTest.CloseBeforeOpenIsNotFatal
41: [ OK ] TngTest.CloseBeforeOpenIsNotFatal (0 ms)
41: [----------] 2 tests from TngTest (2 ms total)
41:
41: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest
41: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0
41: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 (3 ms)
41: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1
41: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 (3 ms)
41: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2
41: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 (9 ms)
41: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3
41: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 (2 ms)
41: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest (20 ms total)
41:
41: [----------] Global test environment tear-down
41: [==========] 33 tests from 8 test cases ran. (88 ms total)
41: [ PASSED ] 33 tests.
41/52 Test #41: FileIOTests ......................... Passed 0.16 sec
test 42
Start 42: SelectionUnitTests
42: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/selection-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/SelectionUnitTests.xml"
42: Test timeout computed to be: 30
42: [==========] Running 192 tests from 11 test cases.
42: [----------] Global test environment set-up.
42: [----------] 1 test from IndexGroupTest
42: [ RUN ] IndexGroupTest.RemovesDuplicates
42: [ OK ] IndexGroupTest.RemovesDuplicates (0 ms)
42: [----------] 1 test from IndexGroupTest (1 ms total)
42:
42: [----------] 15 tests from IndexBlockTest
42: [ RUN ] IndexBlockTest.CreatesUnknownBlock
42: [ OK ] IndexBlockTest.CreatesUnknownBlock (1 ms)
42: [ RUN ] IndexBlockTest.CreatesAtomBlock
42: [ OK ] IndexBlockTest.CreatesAtomBlock (1 ms)
42: [ RUN ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology
42: [ OK ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology (1 ms)
42: [ RUN ] IndexBlockTest.CreatesResidueBlocksForComplexTopology
42: [ OK ] IndexBlockTest.CreatesResidueBlocksForComplexTopology (2 ms)
42: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology
42: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology (1 ms)
42: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology
42: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology (1 ms)
42: [ RUN ] IndexBlockTest.CreatesSingleBlock
42: [ OK ] IndexBlockTest.CreatesSingleBlock (0 ms)
42: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksPositive
42: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksPositive (0 ms)
42: [ RUN ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive
42: [ OK ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive (0 ms)
42: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksNegative
42: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksNegative (0 ms)
42: [ RUN ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial
42: [ OK ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial (0 ms)
42: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive
42: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive (0 ms)
42: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative
42: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative (0 ms)
42: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive
42: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive (1 ms)
42: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative
42: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative (0 ms)
42: [----------] 15 tests from IndexBlockTest (11 ms total)
42:
42: [----------] 11 tests from IndexMapTest
42: [ RUN ] IndexMapTest.InitializesAtomBlock
42: [ OK ] IndexMapTest.InitializesAtomBlock (0 ms)
42: [ RUN ] IndexMapTest.InitializesOrgIdGroupAtom
42: [ OK ] IndexMapTest.InitializesOrgIdGroupAtom (1 ms)
42: [ RUN ] IndexMapTest.InitializesOrgIdGroupSingle
42: [ OK ] IndexMapTest.InitializesOrgIdGroupSingle (1 ms)
42: [ RUN ] IndexMapTest.InitializesOrgIdGroupResidue
42: [ OK ] IndexMapTest.InitializesOrgIdGroupResidue (1 ms)
42: [ RUN ] IndexMapTest.InitializesOrgIdGroupMolecule
42: [ OK ] IndexMapTest.InitializesOrgIdGroupMolecule (0 ms)
42: [ RUN ] IndexMapTest.InitializesOrgIdGroupAll
42: [ OK ] IndexMapTest.InitializesOrgIdGroupAll (0 ms)
42: [ RUN ] IndexMapTest.InitializesMoleculeBlock
42: [ OK ] IndexMapTest.InitializesMoleculeBlock (1 ms)
42: [ RUN ] IndexMapTest.MapsSingleBlock
42: [ OK ] IndexMapTest.MapsSingleBlock (1 ms)
42: [ RUN ] IndexMapTest.MapsResidueBlocks
42: [ OK ] IndexMapTest.MapsResidueBlocks (1 ms)
42: [ RUN ] IndexMapTest.MapsResidueBlocksWithMask
42: [ OK ] IndexMapTest.MapsResidueBlocksWithMask (2 ms)
42: [ RUN ] IndexMapTest.HandlesMultipleRequests
42: [ OK ] IndexMapTest.HandlesMultipleRequests (3 ms)
42: [----------] 11 tests from IndexMapTest (12 ms total)
42:
42: [----------] 3 tests from IndexGroupsAndNamesTest
42: [ RUN ] IndexGroupsAndNamesTest.containsNames
42: [ OK ] IndexGroupsAndNamesTest.containsNames (0 ms)
42: [ RUN ] IndexGroupsAndNamesTest.throwsWhenNameMissing
42: [ OK ] IndexGroupsAndNamesTest.throwsWhenNameMissing (1 ms)
42: [ RUN ] IndexGroupsAndNamesTest.groupIndicesCorrect
42: [ OK ] IndexGroupsAndNamesTest.groupIndicesCorrect (0 ms)
42: [----------] 3 tests from IndexGroupsAndNamesTest (1 ms total)
42:
42: [----------] 15 tests from NeighborhoodSearchTest
42: [ RUN ] NeighborhoodSearchTest.SimpleSearch
42: [ OK ] NeighborhoodSearchTest.SimpleSearch (75 ms)
42: [ RUN ] NeighborhoodSearchTest.SimpleSearchXY
42: [ OK ] NeighborhoodSearchTest.SimpleSearchXY (77 ms)
42: [ RUN ] NeighborhoodSearchTest.GridSearchBox
42: [ OK ] NeighborhoodSearchTest.GridSearchBox (13 ms)
42: [ RUN ] NeighborhoodSearchTest.GridSearchTriclinic
42: [ OK ] NeighborhoodSearchTest.GridSearchTriclinic (49 ms)
42: [ RUN ] NeighborhoodSearchTest.GridSearch2DPBC
42: [ OK ] NeighborhoodSearchTest.GridSearch2DPBC (24 ms)
42: [ RUN ] NeighborhoodSearchTest.GridSearchNoPBC
42: [ OK ] NeighborhoodSearchTest.GridSearchNoPBC (14 ms)
42: [ RUN ] NeighborhoodSearchTest.GridSearchXYBox
42: [ OK ] NeighborhoodSearchTest.GridSearchXYBox (14 ms)
42: [ RUN ] NeighborhoodSearchTest.SimpleSelfPairsSearch
42: [ OK ] NeighborhoodSearchTest.SimpleSelfPairsSearch (1 ms)
42: [ RUN ] NeighborhoodSearchTest.GridSelfPairsSearch
42: [ OK ] NeighborhoodSearchTest.GridSelfPairsSearch (220 ms)
42: [ RUN ] NeighborhoodSearchTest.HandlesConcurrentSearches
42: [ OK ] NeighborhoodSearchTest.HandlesConcurrentSearches (1 ms)
42: [ RUN ] NeighborhoodSearchTest.HandlesNoPBC
42: [ OK ] NeighborhoodSearchTest.HandlesNoPBC (0 ms)
42: [ RUN ] NeighborhoodSearchTest.HandlesNullPBC
42: [ OK ] NeighborhoodSearchTest.HandlesNullPBC (0 ms)
42: [ RUN ] NeighborhoodSearchTest.HandlesSkippingPairs
42: [ OK ] NeighborhoodSearchTest.HandlesSkippingPairs (0 ms)
42: [ RUN ] NeighborhoodSearchTest.SimpleSearchExclusions
42: [ OK ] NeighborhoodSearchTest.SimpleSearchExclusions (18 ms)
42: [ RUN ] NeighborhoodSearchTest.GridSearchExclusions
42: [ OK ] NeighborhoodSearchTest.GridSearchExclusions (4 ms)
42: [----------] 15 tests from NeighborhoodSearchTest (510 ms total)
42:
42: [----------] 12 tests from PositionCalculationTest
42: [ RUN ] PositionCalculationTest.ComputesAtomPositions
42: [ OK ] PositionCalculationTest.ComputesAtomPositions (2 ms)
42: [ RUN ] PositionCalculationTest.ComputesResidueCOGPositions
42: [ OK ] PositionCalculationTest.ComputesResidueCOGPositions (2 ms)
42: [ RUN ] PositionCalculationTest.ComputesResidueCOMPositions
42: [ OK ] PositionCalculationTest.ComputesResidueCOMPositions (1 ms)
42: [ RUN ] PositionCalculationTest.ComputesGroupCOGPositions
42: [ OK ] PositionCalculationTest.ComputesGroupCOGPositions (1 ms)
42: [ RUN ] PositionCalculationTest.ComputesGroupCOMPositions
42: [ OK ] PositionCalculationTest.ComputesGroupCOMPositions (1 ms)
42: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteWhole
42: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteWhole (1 ms)
42: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteMax
42: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteMax (1 ms)
42: [ RUN ] PositionCalculationTest.ComputesPositionMask
42: [ OK ] PositionCalculationTest.ComputesPositionMask (1 ms)
42: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms
42: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms (1 ms)
42: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms2
42: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms2 (1 ms)
42: [ RUN ] PositionCalculationTest.HandlesIdenticalStaticCalculations
42: [ OK ] PositionCalculationTest.HandlesIdenticalStaticCalculations (2 ms)
42: [ RUN ] PositionCalculationTest.HandlesOverlappingStaticCalculations
42: [ OK ] PositionCalculationTest.HandlesOverlappingStaticCalculations (1 ms)
42: [----------] 12 tests from PositionCalculationTest (17 ms total)
42:
42: [----------] 29 tests from SelectionCollectionTest
42: [ RUN ] SelectionCollectionTest.HandlesNoSelections
42: [ OK ] SelectionCollectionTest.HandlesNoSelections (2 ms)
42: [ RUN ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType
42: [ OK ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType (3 ms)
42: [ RUN ] SelectionCollectionTest.HandlesVelocityAndForceRequests
42: [ OK ] SelectionCollectionTest.HandlesVelocityAndForceRequests (1 ms)
42: [ RUN ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry
42: [ OK ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry (2 ms)
42: [ RUN ] SelectionCollectionTest.ParsesSelectionsFromFile
42: [ OK ] SelectionCollectionTest.ParsesSelectionsFromFile (2 ms)
42: [ RUN ] SelectionCollectionTest.HandlesAtypicalWhitespace
42: [ OK ] SelectionCollectionTest.HandlesAtypicalWhitespace (1 ms)
42: [ RUN ] SelectionCollectionTest.HandlesInvalidRegularExpressions
42: [ OK ] SelectionCollectionTest.HandlesInvalidRegularExpressions (2 ms)
42: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue
42: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue (2 ms)
42: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue2
42: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue2 (1 ms)
42: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue3
42: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue3 (2 ms)
42: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1
42: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 (1 ms)
42: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2
42: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 (2 ms)
42: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1
42: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 (1 ms)
42: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2
42: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 (2 ms)
42: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReference
42: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReference (2 ms)
42: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed
42: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed (1 ms)
42: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup
42: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup (2 ms)
42: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed
42: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed (1 ms)
42: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2
42: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 (2 ms)
42: [ RUN ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo
42: [ OK ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo (2 ms)
42: [ RUN ] SelectionCollectionTest.RecoversFromMissingAtomTypes
42: [ OK ] SelectionCollectionTest.RecoversFromMissingAtomTypes (2 ms)
42: [ RUN ] SelectionCollectionTest.RecoversFromMissingPDBInfo
42: [ OK ] SelectionCollectionTest.RecoversFromMissingPDBInfo (2 ms)
42: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation
42: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation (1 ms)
42: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation2
42: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation2 (1 ms)
42: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation3
42: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation3 (3 ms)
42: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets
42: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets (2 ms)
42: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2
42: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 (1 ms)
42: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3
42: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 (1 ms)
42: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4
42: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 (2 ms)
42: [----------] 29 tests from SelectionCollectionTest (52 ms total)
42:
42: [----------] 14 tests from SelectionCollectionInteractiveTest
42: [ RUN ] SelectionCollectionInteractiveTest.HandlesBasicInput
42: [ OK ] SelectionCollectionInteractiveTest.HandlesBasicInput (3 ms)
42: [ RUN ] SelectionCollectionInteractiveTest.HandlesContinuation
42: [ OK ] SelectionCollectionInteractiveTest.HandlesContinuation (2 ms)
42: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput
42: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput (2 ms)
42: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput
42: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput (2 ms)
42: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups
42: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups (4 ms)
42: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections
42: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections (3 ms)
42: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus
42: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus (3 ms)
42: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus
42: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus (2 ms)
42: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus
42: [ OK ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus (3 ms)
42: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline
42: [ OK ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline (2 ms)
42: [ RUN ] SelectionCollectionInteractiveTest.HandlesEmptySelections
42: [ OK ] SelectionCollectionInteractiveTest.HandlesEmptySelections (3 ms)
42: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine
42: [ OK ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine (2 ms)
42: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput
42: [ OK ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput (2 ms)
42: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively
42: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively (2 ms)
42: [----------] 14 tests from SelectionCollectionInteractiveTest (35 ms total)
42:
42: [----------] 66 tests from SelectionCollectionDataTest
42: [ RUN ] SelectionCollectionDataTest.HandlesAllNone
42: [ OK ] SelectionCollectionDataTest.HandlesAllNone (2 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesAtomnr
42: [ OK ] SelectionCollectionDataTest.HandlesAtomnr (2 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesResnr
42: [ OK ] SelectionCollectionDataTest.HandlesResnr (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesResIndex
42: [ OK ] SelectionCollectionDataTest.HandlesResIndex (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesMolIndex
42: [ OK ] SelectionCollectionDataTest.HandlesMolIndex (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesAtomname
42: [ OK ] SelectionCollectionDataTest.HandlesAtomname (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesPdbAtomname
42: [ OK ] SelectionCollectionDataTest.HandlesPdbAtomname (4 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesAtomtype
42: [ OK ] SelectionCollectionDataTest.HandlesAtomtype (2 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesChain
42: [ OK ] SelectionCollectionDataTest.HandlesChain (2 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesMass
42: [ OK ] SelectionCollectionDataTest.HandlesMass (2 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesCharge
42: [ OK ] SelectionCollectionDataTest.HandlesCharge (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesAltLoc
42: [ OK ] SelectionCollectionDataTest.HandlesAltLoc (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesInsertCode
42: [ OK ] SelectionCollectionDataTest.HandlesInsertCode (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesOccupancy
42: [ OK ] SelectionCollectionDataTest.HandlesOccupancy (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesBeta
42: [ OK ] SelectionCollectionDataTest.HandlesBeta (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesResname
42: [ OK ] SelectionCollectionDataTest.HandlesResname (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesCoordinateKeywords
42: [ OK ] SelectionCollectionDataTest.HandlesCoordinateKeywords (5 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesSameResidue
42: [ OK ] SelectionCollectionDataTest.HandlesSameResidue (2 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesSameResidueName
42: [ OK ] SelectionCollectionDataTest.HandlesSameResidueName (2 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesPositionKeywords
42: [ OK ] SelectionCollectionDataTest.HandlesPositionKeywords (8 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesDistanceKeyword
42: [ OK ] SelectionCollectionDataTest.HandlesDistanceKeyword (4 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesMinDistanceKeyword
42: [ OK ] SelectionCollectionDataTest.HandlesMinDistanceKeyword (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesWithinKeyword
42: [ OK ] SelectionCollectionDataTest.HandlesWithinKeyword (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword
42: [ OK ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword (25 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesPermuteModifier
42: [ OK ] SelectionCollectionDataTest.HandlesPermuteModifier (10 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesPlusModifier
42: [ OK ] SelectionCollectionDataTest.HandlesPlusModifier (10 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesMergeModifier
42: [ OK ] SelectionCollectionDataTest.HandlesMergeModifier (11 ms)
42: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndCharges
42: [ OK ] SelectionCollectionDataTest.ComputesMassesAndCharges (9 ms)
42: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology
42: [ OK ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology (4 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets
42: [ OK ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets (5 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesSelectionNames
42: [ OK ] SelectionCollectionDataTest.HandlesSelectionNames (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections
42: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections (5 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed
42: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections
42: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections (7 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed
42: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed (5 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositions
42: [ OK ] SelectionCollectionDataTest.HandlesConstantPositions (2 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers
42: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers (2 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesWithinConstantPositions
42: [ OK ] SelectionCollectionDataTest.HandlesWithinConstantPositions (4 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges
42: [ OK ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges (2 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingRealRanges
42: [ OK ] SelectionCollectionDataTest.HandlesOverlappingRealRanges (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode
42: [ OK ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesWildcardMatching
42: [ OK ] SelectionCollectionDataTest.HandlesWildcardMatching (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesRegexMatching
42: [ OK ] SelectionCollectionDataTest.HandlesRegexMatching (4 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesBasicBoolean
42: [ OK ] SelectionCollectionDataTest.HandlesBasicBoolean (5 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters
42: [ OK ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters (5 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions
42: [ OK ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame
42: [ OK ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords
42: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords (4 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods
42: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods (4 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositions
42: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositions (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic
42: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesNumericComparisons
42: [ OK ] SelectionCollectionDataTest.HandlesNumericComparisons (7 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesArithmeticExpressions
42: [ OK ] SelectionCollectionDataTest.HandlesArithmeticExpressions (7 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesNumericVariables
42: [ OK ] SelectionCollectionDataTest.HandlesNumericVariables (5 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesComplexNumericVariables
42: [ OK ] SelectionCollectionDataTest.HandlesComplexNumericVariables (6 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariables
42: [ OK ] SelectionCollectionDataTest.HandlesPositionVariables (6 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariableInModifier
42: [ OK ] SelectionCollectionDataTest.HandlesPositionVariableInModifier (5 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionInVariable
42: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionInVariable (5 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables
42: [ OK ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables (5 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis
42: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis (5 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables
42: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables
42: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesUnusedVariables
42: [ OK ] SelectionCollectionDataTest.HandlesUnusedVariables (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups
42: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups
42: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups (3 ms)
42: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2
42: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 (4 ms)
42: [----------] 66 tests from SelectionCollectionDataTest (313 ms total)
42:
42: [----------] 17 tests from SelectionOptionTest
42: [ RUN ] SelectionOptionTest.ParsesSimpleSelection
42: [ OK ] SelectionOptionTest.ParsesSimpleSelection (2 ms)
42: [ RUN ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired
42: [ OK ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired (1 ms)
42: [ RUN ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired
42: [ OK ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired (2 ms)
42: [ RUN ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired
42: [ OK ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired (2 ms)
42: [ RUN ] SelectionOptionTest.ChecksEmptySelections
42: [ OK ] SelectionOptionTest.ChecksEmptySelections (2 ms)
42: [ RUN ] SelectionOptionTest.ChecksEmptyDelayedSelections
42: [ OK ] SelectionOptionTest.ChecksEmptyDelayedSelections (1 ms)
42: [ RUN ] SelectionOptionTest.HandlesTooManySelections
42: [ OK ] SelectionOptionTest.HandlesTooManySelections (1 ms)
42: [ RUN ] SelectionOptionTest.HandlesTooFewSelections
42: [ OK ] SelectionOptionTest.HandlesTooFewSelections (2 ms)
42: [ RUN ] SelectionOptionTest.HandlesDefaultSelectionText
42: [ OK ] SelectionOptionTest.HandlesDefaultSelectionText (1 ms)
42: [ RUN ] SelectionOptionTest.HandlesAdjuster
42: [ OK ] SelectionOptionTest.HandlesAdjuster (1 ms)
42: [ RUN ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster
42: [ OK ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster (1 ms)
42: [ RUN ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster
42: [ OK ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster (2 ms)
42: [ RUN ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster
42: [ OK ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster (1 ms)
42: [ RUN ] SelectionOptionTest.HandlesDelayedRequiredSelection
42: [ OK ] SelectionOptionTest.HandlesDelayedRequiredSelection (1 ms)
42: [ RUN ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections
42: [ OK ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections (1 ms)
42: [ RUN ] SelectionOptionTest.HandlesDelayedOptionalSelection
42: [ OK ] SelectionOptionTest.HandlesDelayedOptionalSelection (1 ms)
42: [ RUN ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster
42: [ OK ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster (2 ms)
42: [----------] 17 tests from SelectionOptionTest (24 ms total)
42:
42: [----------] 9 tests from SelectionFileOptionTest
42: [ RUN ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile
42: [ OK ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile (1 ms)
42: [ RUN ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions
42: [ OK ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions (2 ms)
42: [ RUN ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile
42: [ OK ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile (1 ms)
42: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFile
42: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFile (2 ms)
42: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet
42: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet (1 ms)
42: [ RUN ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile
42: [ OK ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile (2 ms)
42: [ RUN ] SelectionFileOptionTest.GivesErrorWithNoFile
42: [ OK ] SelectionFileOptionTest.GivesErrorWithNoFile (1 ms)
42: [ RUN ] SelectionFileOptionTest.GivesErrorWithNonExistentFile
42: [ OK ] SelectionFileOptionTest.GivesErrorWithNonExistentFile (1 ms)
42: [ RUN ] SelectionFileOptionTest.GivesErrorWithMultipleFiles
42: [ OK ] SelectionFileOptionTest.GivesErrorWithMultipleFiles (2 ms)
42: [----------] 9 tests from SelectionFileOptionTest (13 ms total)
42:
42: [----------] Global test environment tear-down
42: [==========] 192 tests from 11 test cases ran. (992 ms total)
42: [ PASSED ] 192 tests.
42/52 Test #42: SelectionUnitTests .................. Passed 1.08 sec
test 43
Start 43: MdrunTests
43: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrun-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunTests.xml"
43: Test timeout computed to be: 600
43: [==========] Running 96 tests from 23 test cases.
43: [----------] Global test environment set-up.
43: [----------] 4 tests from DensityFittingTest
43: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct
43: Setting the LD random seed to -1491273094
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group rest is 33.00
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43:
43: Steepest Descents:
43: Tolerance (Fmax) = 1.00000e+01
43: Number of steps = 2
43:
43: Energy minimization reached the maximum number of steps before the forces
43: reached the requested precision Fmax < 10.
43:
43: writing lowest energy coordinates.
43:
43: Steepest Descents did not converge to Fmax < 10 in 3 steps.
43: Potential Energy = -3.85654101644806e+03
43: Maximum force = 2.88468568366558e+03 on atom 3
43: Norm of force = 1.07544474716821e+03
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Last energy frame read 2 time 2.000 This run will generate roughly 0 Mb of data
43: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct (92 ms)
43: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy
43: Setting the LD random seed to -1958256933
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group rest is 33.00
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43:
43: Steepest Descents:
43: Tolerance (Fmax) = 1.00000e+01
43: Number of steps = 2
43:
43: Energy minimization reached the maximum number of steps before the forces
43: reached the requested precision Fmax < 10.
43:
43: writing lowest energy coordinates.
43:
43: Steepest Descents did not converge to Fmax < 10 in 3 steps.
43: Potential Energy = -2.71386626596691e+04
43: Maximum force = 4.34097106676756e+03 on atom 2
43: Norm of force = 1.25497916295893e+03
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Last energy frame read 2 time 2.000 This run will generate roughly 0 Mb of data
43: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy (38 ms)
43: [ RUN ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch
43:
43: [WARNING] /<<PKGBUILDDIR>>/src/external/googletest/googletest/src/gtest-death-test.cc:836:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads.
43: [ OK ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch (38 ms)
43: [ RUN ] DensityFittingTest.CheckpointWorks
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (2)
43:
43: Setting the LD random seed to -921534777
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group rest is 33.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]:
43: NVE simulation: will use the initial temperature of 68.810 K for
43: determining the Verlet buffer size
43:
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 2 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 68.8096 K
43: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.240 0.120 199.6
43: (ns/day) (hour/ns)
43: Performance: 2.155 11.138
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Overriding nsteps with value passed on the command line: 4 steps, 0.004 ps
43: Can not increase nstlist because an NVE ensemble is used
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 6 steps, 0.0 ps (continuing from step 2, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.200 0.100 199.5
43: (ns/day) (hour/ns)
43: Performance: 4.304 5.576
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.002
Last energy frame read 1 time 0.002 [ OK ] DensityFittingTest.CheckpointWorks (267 ms)
43: [----------] 4 tests from DensityFittingTest (435 ms total)
43:
43: [----------] 3 tests from GromppTest
43: [ RUN ] GromppTest.EmptyMdpFileWorks
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]:
43: For a correct single-point energy evaluation with nsteps = 0, use
43: continuation = yes to avoid constraining the input coordinates.
43:
43: Setting the LD random seed to 550118438
43: Generated 8 of the 10 non-bonded parameter combinations
43: Excluding 2 bonded neighbours molecule type 'Methanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group rest is 12.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]:
43: NVE simulation: will use the initial temperature of 1046.791 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
43: Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: [ OK ] GromppTest.EmptyMdpFileWorks (23 ms)
43: [ RUN ] GromppTest.SimulatedAnnealingWorks
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]:
43: For a correct single-point energy evaluation with nsteps = 0, use
43: continuation = yes to avoid constraining the input coordinates.
43:
43: Setting the LD random seed to 2130366773
43: Generated 8 of the 10 non-bonded parameter combinations
43: Excluding 2 bonded neighbours molecule type 'Methanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Simulated annealing for group rest: Periodic, 4 timepoints
43: Time (ps) Temperature (K)
43: 0.0 298.0
43: 2.0 320.0
43: 4.0 320.0
43: 6.0 298.0
43: Number of degrees of freedom in T-Coupling group rest is 12.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]:
43: NVE simulation: will use the initial temperature of 1046.791 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
43: Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: [ OK ] GromppTest.SimulatedAnnealingWorks (23 ms)
43: [ RUN ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]:
43: For a correct single-point energy evaluation with nsteps = 0, use
43: continuation = yes to avoid constraining the input coordinates.
43:
43: Setting the LD random seed to -1118320313
43: Generated 8 of the 10 non-bonded parameter combinations
43: Excluding 2 bonded neighbours molecule type 'Methanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Simulated annealing for group Methanol: Single, 3 timepoints
43: Time (ps) Temperature (K)
43: 0.0 298.0
43: 3.0 280.0
43: 6.0- 270.0
43: Simulated annealing for group SOL: Periodic, 4 timepoints
43: Time (ps) Temperature (K)
43: 0.0 298.0
43: 2.0 320.0
43: 4.0 320.0
43: 6.0 298.0
43: Number of degrees of freedom in T-Coupling group Methanol is 7.20
43: Number of degrees of freedom in T-Coupling group SOL is 4.80
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]:
43: NVE simulation: will use the initial temperature of 1046.791 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
43: Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: [ OK ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups (23 ms)
43: [----------] 3 tests from GromppTest (70 ms total)
43:
43: [----------] 1 test from MdrunTest
43: [ RUN ] MdrunTest.WritesHelp
43: [ OK ] MdrunTest.WritesHelp (14 ms)
43: [----------] 1 test from MdrunTest (14 ms total)
43:
43: [----------] 1 test from OriresTest
43: [ RUN ] OriresTest.OriresCanRun
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun_input.mdp]:
43: The Berendsen thermostat does not generate the correct kinetic energy
43: distribution. You might want to consider using the V-rescale thermostat.
43:
43: Setting the LD random seed to -1342872758
43: Generated 2145 of the 2145 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 2145 of the 2145 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 518.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Orientation restraints only supports a single rank. Choosing to use only a single thread-MPI rank.
43: Changing nstlist from 10 to 25, rlist from 1.054 to 1.164
43:
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'GUANINE NUCLEOTIDE-BINDING PROTEIN G(T), ALPHA-1'
43: 10 steps, 0.0 ps.
43: turning H bonds into constraints...
43: turning H bonds into constraints...
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
43: Calculated rlist for 1x1 atom pair-list as 1.073 nm, buffer size 0.073 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.054 nm, buffer size 0.054 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.358 0.179 199.5
43: (ns/day) (hour/ns)
43: Performance: 10.593 2.266
43: [ OK ] OriresTest.OriresCanRun (2107 ms)
43: [----------] 1 test from OriresTest (2107 ms total)
43:
43: [----------] 3 tests from PmeTest
43: [ RUN ] PmeTest.ReproducesEnergies
43: Setting the LD random seed to -525292096
43: Generated 8 of the 10 non-bonded parameter combinations
43: Excluding 2 bonded neighbours molecule type 'Methanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group rest is 12.00
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
43: NVE simulation: will use the initial temperature of 1046.791 K for
43: determining the Verlet buffer size
43:
43: Estimate for the relative computational load of the PME mesh part: 1.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
43: The optimal PME mesh load for parallel simulations is below 0.5
43: and for highly parallel simulations between 0.25 and 0.33,
43: for higher performance, increase the cut-off and the PME grid spacing.
43:
43:
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc-and-methanol'
43: 20 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
43: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: Calculating fourier grid dimensions for X Y Z
43: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.614 0.307 199.8
43: (ns/day) (hour/ns)
43: Performance: 5.907 4.063
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeAuto.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc-and-methanol'
43: 20 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.614 0.307 199.8
43: (ns/day) (hour/ns)
43: Performance: 5.910 4.061
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpu.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43:
43: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
43: starting mdrun 'spc-and-methanol'
43: 20 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.607 0.304 199.8
43: (ns/day) (hour/ns)
43: Performance: 5.975 4.017
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpuTune.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 [ OK ] PmeTest.ReproducesEnergies (1090 ms)
43: [ RUN ] PmeTest.ScalesTheBox
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
43: For a correct single-point energy evaluation with nsteps = 0, use
43: continuation = yes to avoid constraining the input coordinates.
43:
43: Setting the LD random seed to -825641582
43: Generated 8 of the 10 non-bonded parameter combinations
43: Excluding 2 bonded neighbours molecule type 'Methanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group rest is 12.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
43: NVE simulation: will use the initial temperature of 1046.791 K for
43: determining the Verlet buffer size
43:
43: Estimate for the relative computational load of the PME mesh part: 1.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
43: The optimal PME mesh load for parallel simulations is below 0.5
43: and for highly parallel simulations between 0.25 and 0.33,
43: for higher performance, increase the cut-off and the PME grid spacing.
43:
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc-and-methanol'
43: 0 steps, 0.0 ps.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.020 0.010 193.9
43: (ns/day) (hour/ns)
43: Performance: 8.420 2.850
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_spc-and-methanol_PmeOnCpu.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
43: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: Calculating fourier grid dimensions for X Y Z
43: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107
43: This run will generate roughly 0 Mb of data
43: [ OK ] PmeTest.ScalesTheBox (72 ms)
43: [ RUN ] PmeTest.ScalesTheBoxWithWalls
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
43: For a correct single-point energy evaluation with nsteps = 0, use
43: continuation = yes to avoid constraining the input coordinates.
43:
43: Setting the LD random seed to -155486720
43: Generated 8 of the 10 non-bonded parameter combinations
43: Excluding 2 bonded neighbours molecule type 'Methanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Searching the wall atom type(s)
43: Number of degrees of freedom in T-Coupling group rest is 13.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
43: NVE simulation: will use the initial temperature of 966.268 K for
43: determining the Verlet buffer size
43:
43: Estimate for the relative computational load of the PME mesh part: 1.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
43: The optimal PME mesh load for parallel simulations is below 0.5
43: and for highly parallel simulations between 0.25 and 0.33,
43: for higher performance, increase the cut-off and the PME grid spacing.
43:
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc-and-methanol'
43: 0 steps, 0.0 ps.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.098 0.049 198.4
43: (ns/day) (hour/ns)
43: Performance: 1.757 13.658
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_spc-and-methanol_PmeOnCpu.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K
43: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: Calculating fourier grid dimensions for X Y Z
43: Using a fourier grid of 28x28x128, spacing 0.107 0.107 0.118
43: This run will generate roughly 0 Mb of data
43: [ OK ] PmeTest.ScalesTheBoxWithWalls (205 ms)
43: [----------] 3 tests from PmeTest (1368 ms total)
43:
43: [----------] 1 test from CompelTest
43: [ RUN ] CompelTest.SwapCanRun
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]:
43: The Berendsen thermostat does not generate the correct kinetic energy
43: distribution. You might want to consider using the V-rescale thermostat.
43:
43: Setting the LD random seed to 660793480
43: Generated 330891 of the 330891 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 330891 of the 330891 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'Protein'
43: Excluding 3 bonded neighbours molecule type 'OCT'
43: Excluding 1 bonded neighbours molecule type 'NA'
43: Excluding 1 bonded neighbours molecule type 'CL'
43: Excluding 3 bonded neighbours molecule type 'Protein'
43: Excluding 3 bonded neighbours molecule type 'OCT'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Split0 group 'Ch0' contains 83 atoms.
43: Split1 group 'Ch1' contains 83 atoms.
43: Solvent group 'SOL' contains 11931 atoms.
43: Swap group 'NA+' contains 19 atoms.
43: Swap group 'CL-' contains 19 atoms.
43: Number of degrees of freedom in T-Coupling group System is 27869.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]:
43: Removing center of mass motion in the presence of position restraints
43: might cause artifacts. When you are using position restraints to
43: equilibrate a macro-molecule, the artifacts are usually negligible.
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: SWAP: Determining initial numbers of ions per compartment.
43: SWAP: Setting pointers for checkpoint writing
43: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules
43: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules
43: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules
43: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules
43: starting mdrun 'Channel_coco in octane membrane'
43: 2 steps, 0.0 ps.
43: turning all bonds into constraints...
43: turning all bonds into constraints...
43: turning all bonds into constraints...
43: turning all bonds into constraints...
43: turning all bonds into constraints...
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
43: Calculated rlist for 1x1 atom pair-list as 1.314 nm, buffer size 0.314 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.260 nm, buffer size 0.260 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 1 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 6.679 3.340 200.0
43: (ns/day) (hour/ns)
43: Performance: 0.388 61.852
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Overriding nsteps with value passed on the command line: 2 steps, 0.01 ps
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: SWAP: Setting pointers for checkpoint writing
43: SWAP: Copying channel fluxes from checkpoint file data
43: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules
43: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules
43: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules
43: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules
43: starting mdrun 'Channel_coco in octane membrane'
43: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 5.730 2.865 200.0
43: (ns/day) (hour/ns)
43: Performance: 0.452 53.060
43: [ OK ] CompelTest.SwapCanRun (11931 ms)
43: [----------] 1 test from CompelTest (11932 ms total)
43:
43: [----------] 6 tests from BondedInteractionsTest
43: [ RUN ] BondedInteractionsTest.NormalBondWorks
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]:
43: For a correct single-point energy evaluation with nsteps = 0, use
43: continuation = yes to avoid constraining the input coordinates.
43:
43: Setting the LD random seed to 568464667
43: Generated 3 of the 3 non-bonded parameter combinations
43: Excluding 3 bonded neighbours molecule type 'butane'
43:
43: NOTE 2 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]:
43: In moleculetype 'butane' 2 atoms are not bound by a potential or
43: constraint to any other atom in the same moleculetype. Although
43: technically this might not cause issues in a simulation, this often means
43: that the user forgot to add a bond/potential/constraint or put multiple
43: molecules in the same moleculetype definition by mistake. Run with -v to
43: get information for each atom.
43:
43: Number of degrees of freedom in T-Coupling group rest is 9.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]:
43: NVE simulation with an initial temperature of zero: will use a Verlet
43: buffer of 10%. Check your energy drift!
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
43:
43: Reading frames from gro file 'A single butane', 4 atoms.
43:
Reading frame 0 time 0.000
Last frame 0 time 0.000
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.003 0.002 185.3
43: (ns/day) (hour/ns)
43: Performance: 51.446 0.467
43: This run will generate roughly 0 Mb of data
43: [ OK ] BondedInteractionsTest.NormalBondWorks (37 ms)
43: [ RUN ] BondedInteractionsTest.TabulatedBondWorks
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]:
43: For a correct single-point energy evaluation with nsteps = 0, use
43: continuation = yes to avoid constraining the input coordinates.
43:
43: Setting the LD random seed to -1882824713
43: Generated 3 of the 3 non-bonded parameter combinations
43: Excluding 3 bonded neighbours molecule type 'butane'
43:
43: NOTE 2 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]:
43: In moleculetype 'butane' 2 atoms are not bound by a potential or
43: constraint to any other atom in the same moleculetype. Although
43: technically this might not cause issues in a simulation, this often means
43: that the user forgot to add a bond/potential/constraint or put multiple
43: molecules in the same moleculetype definition by mistake. Run with -v to
43: get information for each atom.
43:
43: Number of degrees of freedom in T-Coupling group rest is 9.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]:
43: NVE simulation with an initial temperature of zero: will use a Verlet
43: buffer of 10%. Check your energy drift!
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
43:
43: Reading frames from gro file 'A single butane', 4 atoms.
43:
Reading frame 0 time 0.000
Last frame 0 time 0.000
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.003 0.002 186.4
43: (ns/day) (hour/ns)
43: Performance: 46.123 0.520
43: This run will generate roughly 0 Mb of data
43: [ OK ] BondedInteractionsTest.TabulatedBondWorks (44 ms)
43: [ RUN ] BondedInteractionsTest.NormalAngleWorks
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]:
43: For a correct single-point energy evaluation with nsteps = 0, use
43: continuation = yes to avoid constraining the input coordinates.
43:
43: Setting the LD random seed to 2018373936
43: Generated 3 of the 3 non-bonded parameter combinations
43: Excluding 3 bonded neighbours molecule type 'butane'
43:
43: NOTE 2 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]:
43: In moleculetype 'butane' 4 atoms are not bound by a potential or
43: constraint to any other atom in the same moleculetype. Although
43: technically this might not cause issues in a simulation, this often means
43: that the user forgot to add a bond/potential/constraint or put multiple
43: molecules in the same moleculetype definition by mistake. Run with -v to
43: get information for each atom.
43:
43: Number of degrees of freedom in T-Coupling group rest is 9.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]:
43: NVE simulation with an initial temperature of zero: will use a Verlet
43: buffer of 10%. Check your energy drift!
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
43:
43: Reading frames from gro file 'A single butane', 4 atoms.
43:
Reading frame 0 time 0.000
Last frame 0 time 0.000
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.003 0.002 185.2
43: (ns/day) (hour/ns)
43: Performance: 50.983 0.471
43: This run will generate roughly 0 Mb of data
43: [ OK ] BondedInteractionsTest.NormalAngleWorks (37 ms)
43: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]:
43: For a correct single-point energy evaluation with nsteps = 0, use
43: continuation = yes to avoid constraining the input coordinates.
43:
43: Setting the LD random seed to 1482933026
43: Generated 3 of the 3 non-bonded parameter combinations
43: Excluding 3 bonded neighbours molecule type 'butane'
43:
43: NOTE 2 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]:
43: In moleculetype 'butane' 4 atoms are not bound by a potential or
43: constraint to any other atom in the same moleculetype. Although
43: technically this might not cause issues in a simulation, this often means
43: that the user forgot to add a bond/potential/constraint or put multiple
43: molecules in the same moleculetype definition by mistake. Run with -v to
43: get information for each atom.
43:
43: Number of degrees of freedom in T-Coupling group rest is 9.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]:
43: NVE simulation with an initial temperature of zero: will use a Verlet
43: buffer of 10%. Check your energy drift!
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
43:
43: Reading frames from gro file 'A single butane', 4 atoms.
43:
Reading frame 0 time 0.000
Last frame 0 time 0.000
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.004 0.002 186.7
43: (ns/day) (hour/ns)
43: Performance: 45.253 0.530
43: This run will generate roughly 0 Mb of data
43: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (52 ms)
43: [ RUN ] BondedInteractionsTest.NormalDihedralWorks
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]:
43: For a correct single-point energy evaluation with nsteps = 0, use
43: continuation = yes to avoid constraining the input coordinates.
43:
43: Setting the LD random seed to 1847754980
43: Generated 3 of the 3 non-bonded parameter combinations
43: Excluding 3 bonded neighbours molecule type 'butane'
43:
43: NOTE 2 [file BondedInteractionsTest_NormalDihedralWorks_butane1.top, line 31]:
43: In moleculetype 'butane' 4 atoms are not bound by a potential or
43: constraint to any other atom in the same moleculetype. Although
43: technically this might not cause issues in a simulation, this often means
43: that the user forgot to add a bond/potential/constraint or put multiple
43: molecules in the same moleculetype definition by mistake. Run with -v to
43: get information for each atom.
43:
43: Number of degrees of freedom in T-Coupling group rest is 9.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]:
43: NVE simulation with an initial temperature of zero: will use a Verlet
43: buffer of 10%. Check your energy drift!
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
43:
43: Reading frames from gro file 'A single butane', 4 atoms.
43:
Reading frame 0 time 0.000
Last frame 0 time 0.000
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.003 0.002 185.9
43: (ns/day) (hour/ns)
43: Performance: 50.585 0.474
43: This run will generate roughly 0 Mb of data
43: [ OK ] BondedInteractionsTest.NormalDihedralWorks (37 ms)
43: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]:
43: For a correct single-point energy evaluation with nsteps = 0, use
43: continuation = yes to avoid constraining the input coordinates.
43:
43: Setting the LD random seed to 535527103
43: Generated 3 of the 3 non-bonded parameter combinations
43: Excluding 3 bonded neighbours molecule type 'butane'
43:
43: NOTE 2 [file BondedInteractionsTest_TabulatedDihedralWorks_butane1.top, line 31]:
43: In moleculetype 'butane' 4 atoms are not bound by a potential or
43: constraint to any other atom in the same moleculetype. Although
43: technically this might not cause issues in a simulation, this often means
43: that the user forgot to add a bond/potential/constraint or put multiple
43: molecules in the same moleculetype definition by mistake. Run with -v to
43: get information for each atom.
43:
43: Number of degrees of freedom in T-Coupling group rest is 9.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]:
43: NVE simulation with an initial temperature of zero: will use a Verlet
43: buffer of 10%. Check your energy drift!
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
43:
43: Reading frames from gro file 'A single butane', 4 atoms.
43:
Reading frame 0 time 0.000
Last frame 0 time 0.000
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.003 0.002 185.8
43: (ns/day) (hour/ns)
43: Performance: 49.298 0.487
43: This run will generate roughly 0 Mb of data
43: [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (45 ms)
43: [----------] 6 tests from BondedInteractionsTest (252 ms total)
43:
43: [----------] 6 tests from MdrunTerminationTest
43: [ RUN ] MdrunTerminationTest.CheckpointRestartAppendsByDefault
43: Setting the LD random seed to -1743174984
43: Generated 3 of the 3 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 3 of the 3 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 9.00
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There was 1 note
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 2 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.196 0.098 199.5
43: (ns/day) (hour/ns)
43: Performance: 2.632 9.117
43: Reading toplogy and stuff from /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Setting nsteps to 4
43: Writing statusfile with starting step 0 and length 4 steps...
43: time 0.000 and length 0.004 ps
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.216 0.108 199.5
43: (ns/day) (hour/ns)
43: Performance: 2.390 10.042
43: [ OK ] MdrunTerminationTest.CheckpointRestartAppendsByDefault (257 ms)
43: [ RUN ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts
43: Setting the LD random seed to 480103117
43: Generated 3 of the 3 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 3 of the 3 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 9.00
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There was 1 note
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 10 to 1, rlist from 1.024 to 1
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 100 steps, 0.1 ps.
43:
43: Step 1: Run time exceeded 0.000 hours, will terminate the run within 2 steps
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.194 0.097 199.5
43: (ns/day) (hour/ns)
43: Performance: 2.666 9.003
43: Reading toplogy and stuff from /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Setting nsteps to 102
43: Writing statusfile with starting step 0 and length 102 steps...
43: time 0.000 and length 0.102 ps
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 102 steps, 0.1 ps (continuing from step 2, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.218 0.109 199.5
43: (ns/day) (hour/ns)
43: Performance: 80.056 0.300
43: [ OK ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (256 ms)
43: [ RUN ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend
43: Setting the LD random seed to 634692763
43: Generated 3 of the 3 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 3 of the 3 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 9.00
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There was 1 note
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 2 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.216 0.108 199.6
43: (ns/day) (hour/ns)
43: Performance: 2.397 10.014
43: Reading toplogy and stuff from /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Setting nsteps to 4
43: Writing statusfile with starting step 0 and length 4 steps...
43: time 0.000 and length 0.004 ps
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.195 0.098 199.7
43: (ns/day) (hour/ns)
43: Performance: 2.658 9.030
43: Reading toplogy and stuff from /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Setting nsteps to 6
43: Writing statusfile with starting step 0 and length 6 steps...
43: time 0.000 and length 0.006 ps
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 6 steps, 0.0 ps (continuing from step 4, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.187 0.093 199.7
43: (ns/day) (hour/ns)
43: Performance: 2.774 8.653
43: Reading toplogy and stuff from /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Setting nsteps to 8
43: Writing statusfile with starting step 0 and length 8 steps...
43: time 0.000 and length 0.008 ps
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 8 steps, 0.0 ps (continuing from step 6, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.193 0.097 199.7
43: (ns/day) (hour/ns)
43: Performance: 2.681 8.952
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 8 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.001 0.001 170.5
43: (ns/day) (hour/ns)
43: Performance: 102.980 0.233
43: [ OK ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend (493 ms)
43: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile
43: Setting the LD random seed to -372432815
43: Generated 3 of the 3 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 3 of the 3 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 9.00
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There was 1 note
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 2 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.207 0.104 199.5
43: (ns/day) (hour/ns)
43: Performance: 2.493 9.629
43: Reading toplogy and stuff from /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Setting nsteps to 4
43: Writing statusfile with starting step 0 and length 4 steps...
43: time 0.000 and length 0.004 ps
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 4 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.194 0.097 199.3
43: (ns/day) (hour/ns)
43: Performance: 4.438 5.408
43: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile (251 ms)
43: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile
43: Setting the LD random seed to -1412112169
43: Generated 3 of the 3 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 3 of the 3 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 9.00
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There was 1 note
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 2 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.195 0.098 199.5
43: (ns/day) (hour/ns)
43: Performance: 2.651 9.053
43: Reading toplogy and stuff from /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Setting nsteps to 4
43: Writing statusfile with starting step 0 and length 4 steps...
43: time 0.000 and length 0.004 ps
43: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile (138 ms)
43: [ RUN ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles
43: Setting the LD random seed to -210390359
43: Generated 3 of the 3 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 3 of the 3 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 9.00
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There was 1 note
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 2 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.183 0.092 199.5
43: (ns/day) (hour/ns)
43: Performance: 2.824 8.498
43: Reading toplogy and stuff from /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Setting nsteps to 4
43: Writing statusfile with starting step 0 and length 4 steps...
43: time 0.000 and length 0.004 ps
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.213 0.107 199.8
43: (ns/day) (hour/ns)
43: Performance: 2.432 9.866
43: [ OK ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles (252 ms)
43: [----------] 6 tests from MdrunTerminationTest (1647 ms total)
43:
43: [----------] 4 tests from MimicTest
43: [ RUN ] MimicTest.OneQuantumMol
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
43: For a correct single-point energy evaluation with nsteps = 0, use
43: continuation = yes to avoid constraining the input coordinates.
43:
43: Setting the LD random seed to -256358280
43: Generated 10 of the 10 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 10 of the 10 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group rest is 21.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
43: NVE simulation with an initial temperature of zero: will use a Verlet
43: buffer of 10%. Check your energy drift!
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
43:
43: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
43:
Reading frame 0 time 0.000
Last frame 0 time 0.000
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.003 0.002 188.5
43: (ns/day) (hour/ns)
43: Performance: 51.792 0.463
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
43: [ OK ] MimicTest.OneQuantumMol (39 ms)
43: [ RUN ] MimicTest.AllQuantumMol
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
43: For a correct single-point energy evaluation with nsteps = 0, use
43: continuation = yes to avoid constraining the input coordinates.
43:
43: Setting the LD random seed to 160187164
43: Generated 10 of the 10 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 10 of the 10 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group rest is 21.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
43: NVE simulation with an initial temperature of zero: will use a Verlet
43: buffer of 10%. Check your energy drift!
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
43:
43: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
43:
Reading frame 0 time 0.000
Last frame 0 time 0.000
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.003 0.002 188.5
43: (ns/day) (hour/ns)
43: Performance: 52.376 0.458
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
43: [ OK ] MimicTest.AllQuantumMol (39 ms)
43: [ RUN ] MimicTest.TwoQuantumMol
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
43: For a correct single-point energy evaluation with nsteps = 0, use
43: continuation = yes to avoid constraining the input coordinates.
43:
43: Setting the LD random seed to -2031843482
43: Generated 10 of the 10 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 10 of the 10 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group rest is 21.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
43: NVE simulation with an initial temperature of zero: will use a Verlet
43: buffer of 10%. Check your energy drift!
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
43:
43: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
43:
Reading frame 0 time 0.000
Last frame 0 time 0.000
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.003 0.002 188.5
43: (ns/day) (hour/ns)
43: Performance: 51.866 0.463
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
43: [ OK ] MimicTest.TwoQuantumMol (39 ms)
43: [ RUN ] MimicTest.BondCuts
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
43: For a correct single-point energy evaluation with nsteps = 0, use
43: continuation = yes to avoid constraining the input coordinates.
43:
43: Setting the LD random seed to 402762614
43: Generated 2211 of the 2211 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 2211 of the 2211 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
43: Number of degrees of freedom in T-Coupling group rest is 66.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
43: NVE simulation: will use the initial temperature of 300.368 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/ala.gro'
43:
43: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms.
43:
Reading frame 0 time 0.000
Last frame 0 time 0.000
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.007 0.003 192.4
43: (ns/day) (hour/ns)
43: Performance: 24.696 0.972
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K
43: Calculated rlist for 1x1 atom pair-list as 1.034 nm, buffer size 0.034 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.025 nm, buffer size 0.025 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: [ OK ] MimicTest.BondCuts (133 ms)
43: [----------] 4 tests from MimicTest (253 ms total)
43:
43: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput
43: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0
43: Setting the LD random seed to -867945342
43: Generated 3 of the 3 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 3 of the 3 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group rest is 9.00
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]:
43: NVE simulation: will use the initial temperature of 2573.591 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 1 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K
43: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.261 0.131 199.5
43: (ns/day) (hour/ns)
43: Performance: 1.323 18.135
43:
Reading frame 0 time 0.000
43: # Atoms 6
43:
Reading frame 1 time 0.001
Last frame 1 time 0.001
43:
43:
43: Item #frames Timestep (ps)
43: Step 2 0.001
43: Time 2 0.001
43: Lambda 0
43: Coords 2 0.001
43: Velocities 0
43: Forces 0
43: Box 2 0.001
43: Checking file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.xtc
43: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 (171 ms)
43: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1
43: Setting the LD random seed to 286984335
43: Generated 3 of the 3 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 3 of the 3 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group rest is 9.00
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]:
43: NVE simulation: will use the initial temperature of 2573.591 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 1 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K
43: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.318 0.159 199.6
43: (ns/day) (hour/ns)
43: Performance: 1.084 22.135
43:
Reading frame 0 time 0.000
43: # Atoms 6
43:
Reading frame 1 time 0.001
Last frame 1 time 0.001
43:
43:
43: Item #frames Timestep (ps)
43: Step 2 0.001
43: Time 2 0.001
43: Lambda 0
43: Coords 2 0.001
43: Velocities 0
43: Forces 0
43: Box 2 0.001
43: Checking file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.xtc
43: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 (200 ms)
43: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2
43: Setting the LD random seed to 948787103
43: Generated 3 of the 3 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 3 of the 3 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group rest is 9.00
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]:
43: NVE simulation: will use the initial temperature of 2573.591 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 1 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K
43: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.274 0.137 199.6
43: (ns/day) (hour/ns)
43: Performance: 1.257 19.087
43:
Reading frame 0 time 0.000
43: # Atoms 3
43:
Reading frame 1 time 0.001
Last frame 1 time 0.001
43:
43:
43: Item #frames Timestep (ps)
43: Step 2 0.001
43: Time 2 0.001
43: Lambda 0
43: Coords 2 0.001
43: Velocities 0
43: Forces 0
43: Box 2 0.001
43: Checking file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.xtc
43: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 (178 ms)
43: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput (549 ms total)
43:
43: [----------] 12 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact
43: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: NVE simulation: will use the initial temperature of 68.810 K for
43: determining the Verlet buffer size
43:
43:
43: There were 3 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: NVE simulation: will use the initial temperature of 68.810 K for
43: determining the Verlet buffer size
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.315 0.158 199.7
43: (ns/day) (hour/ns)
43: Performance: 9.322 2.575
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.309 0.155 198.8
43: (ns/day) (hour/ns)
43: Performance: 5.004 4.796
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.285 0.143 199.7
43: (ns/day) (hour/ns)
43: Performance: 5.453 4.401
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (547 ms)
43: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: NVE simulation: will use the initial temperature of 68.810 K for
43: determining the Verlet buffer size
43:
43:
43: There were 3 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: NVE simulation: will use the initial temperature of 68.810 K for
43: determining the Verlet buffer size
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.331 0.166 199.7
43: (ns/day) (hour/ns)
43: Performance: 8.861 2.709
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.288 0.144 199.8
43: (ns/day) (hour/ns)
43: Performance: 5.399 4.446
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.330 0.165 199.8
43: (ns/day) (hour/ns)
43: Performance: 4.709 5.097
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (566 ms)
43: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.708 nm, buffer size 0.008 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.708 nm, buffer size 0.008 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.708 nm, buffer size 0.008 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.708 nm, buffer size 0.008 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.243 0.122 199.6
43: (ns/day) (hour/ns)
43: Performance: 12.084 1.986
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.312 0.157 199.6
43: (ns/day) (hour/ns)
43: Performance: 4.968 4.831
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.312 0.156 199.7
43: (ns/day) (hour/ns)
43: Performance: 4.974 4.825
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (521 ms)
43: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.298 0.149 199.7
43: (ns/day) (hour/ns)
43: Performance: 9.852 2.436
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.290 0.146 199.5
43: (ns/day) (hour/ns)
43: Performance: 5.343 4.492
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.357 0.179 199.7
43: (ns/day) (hour/ns)
43: Performance: 4.354 5.512
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (556 ms)
43: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 3 of the 3 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 3 of the 3 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 9.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
43: NVE simulation: will use the initial temperature of 2573.591 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 4 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 3 of the 3 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 3 of the 3 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 9.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
43: NVE simulation: will use the initial temperature of 2573.591 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 4 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K
43: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K
43: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.272 0.136 199.6
43: (ns/day) (hour/ns)
43: Performance: 10.798 2.223
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.401 0.201 199.5
43: (ns/day) (hour/ns)
43: Performance: 3.865 6.210
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.290 0.145 199.7
43: (ns/day) (hour/ns)
43: Performance: 5.356 4.481
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (567 ms)
43: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 3 of the 3 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 3 of the 3 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 9.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
43: NVE simulation: will use the initial temperature of 2573.591 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 4 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 3 of the 3 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 3 of the 3 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 9.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
43: NVE simulation: will use the initial temperature of 2573.591 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 4 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K
43: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K
43: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.273 0.137 199.8
43: (ns/day) (hour/ns)
43: Performance: 10.759 2.231
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.247 0.124 199.7
43: (ns/day) (hour/ns)
43: Performance: 6.285 3.819
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.268 0.134 199.8
43: (ns/day) (hour/ns)
43: Performance: 5.793 4.143
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (478 ms)
43: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 3 of the 3 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 3 of the 3 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 9.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 3 of the 3 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 3 of the 3 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 9.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.731 to 0.816
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 0.731 nm, buffer size 0.031 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 0.731 nm, buffer size 0.031 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.312 0.156 199.7
43: (ns/day) (hour/ns)
43: Performance: 9.404 2.552
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.731 to 0.816
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.265 0.133 199.2
43: (ns/day) (hour/ns)
43: Performance: 5.849 4.103
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.731 to 0.816
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.286 0.143 199.6
43: (ns/day) (hour/ns)
43: Performance: 5.424 4.425
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (522 ms)
43: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 3 of the 3 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 3 of the 3 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 9.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 3 of the 3 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 3 of the 3 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 9.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 8 to 40, rlist from 0.754 to 1.017
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.292 0.146 199.7
43: (ns/day) (hour/ns)
43: Performance: 10.044 2.389
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 8 to 40, rlist from 0.754 to 1.017
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.288 0.145 199.2
43: (ns/day) (hour/ns)
43: Performance: 5.376 4.465
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 8 to 40, rlist from 0.754 to 1.017
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.199 0.100 199.5
43: (ns/day) (hour/ns)
43: Performance: 7.804 3.075
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (478 ms)
43: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 2145 of the 2145 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 2145 of the 2145 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
43:
43: NOTE 3 [file unknown]:
43: You are using constraints on all bonds, whereas the forcefield has been
43: parametrized only with constraints involving hydrogen atoms. We suggest
43: using constraints = h-bonds instead, this will also improve performance.
43:
43: Cleaning up constraints and constant bonded interactions with virtual sites
43: Removed 18 Angles with virtual sites, 21 left
43: Removed 10 Proper Dih.s with virtual sites, 44 left
43: Converted 15 Constraints with virtual sites to connections, 7 left
43: Number of degrees of freedom in T-Coupling group System is 23.00
43:
43: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
43: NVE simulation: will use the initial temperature of 456.887 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
43: There are 9 non-linear virtual site constructions. Their contribution to
43: the energy error is approximated. In most cases this does not affect the
43: error significantly.
43:
43:
43: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 6 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 2145 of the 2145 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 2145 of the 2145 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
43:
43: NOTE 3 [file unknown]:
43: You are using constraints on all bonds, whereas the forcefield has been
43: parametrized only with constraints involving hydrogen atoms. We suggest
43: using constraints = h-bonds instead, this will also improve performance.
43:
43: Cleaning up constraints and constant bonded interactions with virtual sites
43: Removed 18 Angles with virtual sites, 21 left
43: Removed 10 Proper Dih.s with virtual sites, 44 left
43: Converted 15 Constraints with virtual sites to connections, 7 left
43: Number of degrees of freedom in T-Coupling group System is 23.00
43:
43: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
43: NVE simulation: will use the initial temperature of 456.887 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
43: There are 9 non-linear virtual site constructions. Their contribution to
43: the energy error is approximated. In most cases this does not affect the
43: error significantly.
43:
43:
43: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 6 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Alanine dipeptide in vacuo'
43: 16 steps, 0.0 ps.
43: turning all bonds into constraints...
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
43: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: turning all bonds into constraints...
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
43: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.327 0.164 199.6
43: (ns/day) (hour/ns)
43: Performance: 8.955 2.680
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Alanine dipeptide in vacuo'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.336 0.168 199.5
43: (ns/day) (hour/ns)
43: Performance: 4.622 5.193
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Alanine dipeptide in vacuo'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.283 0.142 199.5
43: (ns/day) (hour/ns)
43: Performance: 5.476 4.383
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_secondpart.part0002.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8 (768 ms)
43: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 2145 of the 2145 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 2145 of the 2145 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
43:
43: NOTE 3 [file unknown]:
43: You are using constraints on all bonds, whereas the forcefield has been
43: parametrized only with constraints involving hydrogen atoms. We suggest
43: using constraints = h-bonds instead, this will also improve performance.
43:
43: Cleaning up constraints and constant bonded interactions with virtual sites
43: Removed 18 Angles with virtual sites, 21 left
43: Removed 10 Proper Dih.s with virtual sites, 44 left
43: Converted 15 Constraints with virtual sites to connections, 7 left
43: Number of degrees of freedom in T-Coupling group System is 23.00
43:
43: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
43: NVE simulation: will use the initial temperature of 456.887 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
43: There are 9 non-linear virtual site constructions. Their contribution to
43: the energy error is approximated. In most cases this does not affect the
43: error significantly.
43:
43:
43: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 6 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 2145 of the 2145 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 2145 of the 2145 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
43:
43: NOTE 3 [file unknown]:
43: You are using constraints on all bonds, whereas the forcefield has been
43: parametrized only with constraints involving hydrogen atoms. We suggest
43: using constraints = h-bonds instead, this will also improve performance.
43:
43: Cleaning up constraints and constant bonded interactions with virtual sites
43: Removed 18 Angles with virtual sites, 21 left
43: Removed 10 Proper Dih.s with virtual sites, 44 left
43: Converted 15 Constraints with virtual sites to connections, 7 left
43: Number of degrees of freedom in T-Coupling group System is 23.00
43:
43: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
43: NVE simulation: will use the initial temperature of 456.887 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
43: There are 9 non-linear virtual site constructions. Their contribution to
43: the energy error is approximated. In most cases this does not affect the
43: error significantly.
43:
43:
43: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 6 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Alanine dipeptide in vacuo'
43: 16 steps, 0.0 ps.
43: turning all bonds into constraints...
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
43: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: turning all bonds into constraints...
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
43: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 1.417 0.709 199.9
43: (ns/day) (hour/ns)
43: Performance: 2.071 11.586
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Alanine dipeptide in vacuo'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.563 0.282 199.7
43: (ns/day) (hour/ns)
43: Performance: 2.760 8.696
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Alanine dipeptide in vacuo'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.416 0.208 199.7
43: (ns/day) (hour/ns)
43: Performance: 3.734 6.428
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_secondpart.part0002.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9 (1511 ms)
43: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 2145 of the 2145 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 2145 of the 2145 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
43:
43: NOTE 3 [file unknown]:
43: You are using constraints on all bonds, whereas the forcefield has been
43: parametrized only with constraints involving hydrogen atoms. We suggest
43: using constraints = h-bonds instead, this will also improve performance.
43:
43: Cleaning up constraints and constant bonded interactions with virtual sites
43: Removed 18 Angles with virtual sites, 21 left
43: Removed 10 Proper Dih.s with virtual sites, 44 left
43: Converted 15 Constraints with virtual sites to connections, 7 left
43: Number of degrees of freedom in T-Coupling group System is 23.00
43:
43: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
43: There are 9 non-linear virtual site constructions. Their contribution to
43: the energy error is approximated. In most cases this does not affect the
43: error significantly.
43:
43:
43: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 5 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 2145 of the 2145 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 2145 of the 2145 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
43:
43: NOTE 3 [file unknown]:
43: You are using constraints on all bonds, whereas the forcefield has been
43: parametrized only with constraints involving hydrogen atoms. We suggest
43: using constraints = h-bonds instead, this will also improve performance.
43:
43: Cleaning up constraints and constant bonded interactions with virtual sites
43: Removed 18 Angles with virtual sites, 21 left
43: Removed 10 Proper Dih.s with virtual sites, 44 left
43: Converted 15 Constraints with virtual sites to connections, 7 left
43: Number of degrees of freedom in T-Coupling group System is 23.00
43:
43: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
43: There are 9 non-linear virtual site constructions. Their contribution to
43: the energy error is approximated. In most cases this does not affect the
43: error significantly.
43:
43:
43: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 5 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Alanine dipeptide in vacuo'
43: 16 steps, 0.0 ps.
43: turning all bonds into constraints...
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 0.748 nm, buffer size 0.048 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.744 nm, buffer size 0.044 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: turning all bonds into constraints...
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 0.748 nm, buffer size 0.048 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.744 nm, buffer size 0.044 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.347 0.174 199.6
43: (ns/day) (hour/ns)
43: Performance: 8.450 2.840
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Alanine dipeptide in vacuo'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.337 0.169 199.5
43: (ns/day) (hour/ns)
43: Performance: 4.598 5.220
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Alanine dipeptide in vacuo'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.360 0.180 199.6
43: (ns/day) (hour/ns)
43: Performance: 4.312 5.566
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_secondpart.part0002.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10 (1045 ms)
43: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 2145 of the 2145 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 2145 of the 2145 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
43:
43: NOTE 3 [file unknown]:
43: You are using constraints on all bonds, whereas the forcefield has been
43: parametrized only with constraints involving hydrogen atoms. We suggest
43: using constraints = h-bonds instead, this will also improve performance.
43:
43: Cleaning up constraints and constant bonded interactions with virtual sites
43: Removed 18 Angles with virtual sites, 21 left
43: Removed 10 Proper Dih.s with virtual sites, 44 left
43: Converted 15 Constraints with virtual sites to connections, 7 left
43: Number of degrees of freedom in T-Coupling group System is 23.00
43:
43: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
43: There are 9 non-linear virtual site constructions. Their contribution to
43: the energy error is approximated. In most cases this does not affect the
43: error significantly.
43:
43:
43: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 5 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 2145 of the 2145 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 2145 of the 2145 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
43:
43: NOTE 3 [file unknown]:
43: You are using constraints on all bonds, whereas the forcefield has been
43: parametrized only with constraints involving hydrogen atoms. We suggest
43: using constraints = h-bonds instead, this will also improve performance.
43:
43: Cleaning up constraints and constant bonded interactions with virtual sites
43: Removed 18 Angles with virtual sites, 21 left
43: Removed 10 Proper Dih.s with virtual sites, 44 left
43: Converted 15 Constraints with virtual sites to connections, 7 left
43: Number of degrees of freedom in T-Coupling group System is 23.00
43:
43: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
43: There are 9 non-linear virtual site constructions. Their contribution to
43: the energy error is approximated. In most cases this does not affect the
43: error significantly.
43:
43:
43: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 5 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Alanine dipeptide in vacuo'
43: 16 steps, 0.0 ps.
43: turning all bonds into constraints...
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: turning all bonds into constraints...
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.356 0.179 199.6
43: (ns/day) (hour/ns)
43: Performance: 8.226 2.918
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Alanine dipeptide in vacuo'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.499 0.250 199.7
43: (ns/day) (hour/ns)
43: Performance: 3.114 7.707
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Alanine dipeptide in vacuo'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.297 0.149 199.5
43: (ns/day) (hour/ns)
43: Performance: 5.221 4.597
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_secondpart.part0002.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11 (1022 ms)
43: [----------] 12 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact (8581 ms total)
43:
43: [----------] 4 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact
43: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 2485 of the 2485 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 2485 of the 2485 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'nonanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 79.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: NVE simulation: will use the initial temperature of 293.480 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 4 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 2485 of the 2485 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 2485 of the 2485 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'nonanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 79.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: NVE simulation: will use the initial temperature of 293.480 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 4 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun '30 system in water'
43: 16 steps, 0.0 ps.
43: turning H bonds into constraints...
43: turning H bonds into constraints...
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
43: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: turning H bonds into constraints...
43: turning H bonds into constraints...
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
43: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.412 0.206 199.5
43: (ns/day) (hour/ns)
43: Performance: 7.117 3.372
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun '30 system in water'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.549 0.275 199.4
43: (ns/day) (hour/ns)
43: Performance: 2.824 8.499
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun '30 system in water'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.347 0.174 199.5
43: (ns/day) (hour/ns)
43: Performance: 4.475 5.363
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (945 ms)
43: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 2485 of the 2485 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 2485 of the 2485 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'nonanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 79.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: NVE simulation: will use the initial temperature of 293.480 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 4 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 2485 of the 2485 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 2485 of the 2485 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'nonanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 79.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: NVE simulation: will use the initial temperature of 293.480 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 4 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun '30 system in water'
43: 16 steps, 0.0 ps.
43: turning H bonds into constraints...
43: turning H bonds into constraints...
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
43: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: turning H bonds into constraints...
43: turning H bonds into constraints...
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
43: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.437 0.219 199.8
43: (ns/day) (hour/ns)
43: Performance: 6.721 3.571
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun '30 system in water'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.616 0.308 199.9
43: (ns/day) (hour/ns)
43: Performance: 2.524 9.507
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun '30 system in water'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.392 0.196 199.8
43: (ns/day) (hour/ns)
43: Performance: 3.962 6.057
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (1012 ms)
43: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 2485 of the 2485 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 2485 of the 2485 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'nonanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 79.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 2485 of the 2485 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 2485 of the 2485 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'nonanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 79.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun '30 system in water'
43: 16 steps, 0.0 ps.
43: turning H bonds into constraints...
43: turning H bonds into constraints...
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: turning H bonds into constraints...
43: turning H bonds into constraints...
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.383 0.192 199.6
43: (ns/day) (hour/ns)
43: Performance: 7.659 3.134
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun '30 system in water'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.510 0.256 199.4
43: (ns/day) (hour/ns)
43: Performance: 3.041 7.892
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun '30 system in water'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.482 0.242 199.7
43: (ns/day) (hour/ns)
43: Performance: 3.220 7.454
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (1244 ms)
43: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 2485 of the 2485 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 2485 of the 2485 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'nonanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 79.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 2485 of the 2485 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 2485 of the 2485 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'nonanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 79.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun '30 system in water'
43: 16 steps, 0.0 ps.
43: turning H bonds into constraints...
43: turning H bonds into constraints...
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: turning H bonds into constraints...
43: turning H bonds into constraints...
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.567 0.284 199.6
43: (ns/day) (hour/ns)
43: Performance: 5.171 4.641
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun '30 system in water'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.552 0.277 199.5
43: (ns/day) (hour/ns)
43: Performance: 2.808 8.548
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun '30 system in water'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.372 0.186 199.5
43: (ns/day) (hour/ns)
43: Performance: 4.173 5.751
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (1200 ms)
43: [----------] 4 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact (4401 ms total)
43:
43: [----------] 6 tests from NVT/MdrunNoAppendContinuationIsExact
43: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: The Berendsen thermostat does not generate the correct kinetic energy
43: distribution. You might want to consider using the V-rescale thermostat.
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 3 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: The Berendsen thermostat does not generate the correct kinetic energy
43: distribution. You might want to consider using the V-rescale thermostat.
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.469 0.235 199.8
43: (ns/day) (hour/ns)
43: Performance: 6.258 3.835
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.290 0.146 199.5
43: (ns/day) (hour/ns)
43: Performance: 5.342 4.493
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.467 0.234 199.8
43: (ns/day) (hour/ns)
43: Performance: 3.323 7.221
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (698 ms)
43: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.311 0.156 199.7
43: (ns/day) (hour/ns)
43: Performance: 9.426 2.546
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.441 0.221 199.7
43: (ns/day) (hour/ns)
43: Performance: 3.522 6.814
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.285 0.143 199.7
43: (ns/day) (hour/ns)
43: Performance: 5.446 4.407
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (612 ms)
43: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 3 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.552 0.276 199.8
43: (ns/day) (hour/ns)
43: Performance: 5.316 4.515
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.375 0.188 199.6
43: (ns/day) (hour/ns)
43: Performance: 4.143 5.793
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.459 0.230 199.8
43: (ns/day) (hour/ns)
43: Performance: 3.383 7.094
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (786 ms)
43: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: The Berendsen thermostat does not generate the correct kinetic energy
43: distribution. You might want to consider using the V-rescale thermostat.
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 3 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: The Berendsen thermostat does not generate the correct kinetic energy
43: distribution. You might want to consider using the V-rescale thermostat.
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.312 0.156 199.7
43: (ns/day) (hour/ns)
43: Performance: 9.414 2.549
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.241 0.121 199.4
43: (ns/day) (hour/ns)
43: Performance: 6.439 3.727
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.441 0.221 199.8
43: (ns/day) (hour/ns)
43: Performance: 3.520 6.818
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (591 ms)
43: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.265 0.132 199.8
43: (ns/day) (hour/ns)
43: Performance: 11.092 2.164
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.375 0.188 199.8
43: (ns/day) (hour/ns)
43: Performance: 4.142 5.795
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.286 0.143 199.8
43: (ns/day) (hour/ns)
43: Performance: 5.432 4.418
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (554 ms)
43: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.428 0.214 199.8
43: (ns/day) (hour/ns)
43: Performance: 6.856 3.501
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.290 0.146 199.5
43: (ns/day) (hour/ns)
43: Performance: 5.340 4.494
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.290 0.145 199.7
43: (ns/day) (hour/ns)
43: Performance: 5.356 4.481
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (588 ms)
43: [----------] 6 tests from NVT/MdrunNoAppendContinuationIsExact (3831 ms total)
43:
43: [----------] 4 tests from NPH/MdrunNoAppendContinuationIsExact
43: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: NVE simulation: will use the initial temperature of 68.810 K for
43: determining the Verlet buffer size
43:
43:
43: There were 3 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: NVE simulation: will use the initial temperature of 68.810 K for
43: determining the Verlet buffer size
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.363 0.182 199.7
43: (ns/day) (hour/ns)
43: Performance: 8.075 2.972
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.269 0.135 199.4
43: (ns/day) (hour/ns)
43: Performance: 5.768 4.161
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.446 0.223 199.8
43: (ns/day) (hour/ns)
43: Performance: 3.484 6.889
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (622 ms)
43: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: NVE simulation: will use the initial temperature of 68.810 K for
43: determining the Verlet buffer size
43:
43:
43: There were 3 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: NVE simulation: will use the initial temperature of 68.810 K for
43: determining the Verlet buffer size
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.297 0.149 199.6
43: (ns/day) (hour/ns)
43: Performance: 9.874 2.431
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.446 0.224 199.6
43: (ns/day) (hour/ns)
43: Performance: 3.478 6.901
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.334 0.167 199.6
43: (ns/day) (hour/ns)
43: Performance: 4.644 5.168
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (623 ms)
43: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/2
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: NVE simulation: will use the initial temperature of 68.810 K for
43: determining the Verlet buffer size
43:
43:
43: There were 3 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: NVE simulation: will use the initial temperature of 68.810 K for
43: determining the Verlet buffer size
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.644 0.322 199.8
43: (ns/day) (hour/ns)
43: Performance: 4.555 5.269
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.313 0.158 198.7
43: (ns/day) (hour/ns)
43: Performance: 4.933 4.865
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.511 0.256 199.8
43: (ns/day) (hour/ns)
43: Performance: 3.041 7.892
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (822 ms)
43: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/3
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: NVE simulation: will use the initial temperature of 68.810 K for
43: determining the Verlet buffer size
43:
43:
43: There were 3 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: NVE simulation: will use the initial temperature of 68.810 K for
43: determining the Verlet buffer size
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.340 0.170 199.8
43: (ns/day) (hour/ns)
43: Performance: 8.621 2.784
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.449 0.224 199.9
43: (ns/day) (hour/ns)
43: Performance: 3.464 6.929
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.356 0.178 199.8
43: (ns/day) (hour/ns)
43: Performance: 4.363 5.501
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (656 ms)
43: [----------] 4 tests from NPH/MdrunNoAppendContinuationIsExact (2723 ms total)
43:
43: [----------] 12 tests from NPT/MdrunNoAppendContinuationIsExact
43: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: The Berendsen thermostat does not generate the correct kinetic energy
43: distribution. You might want to consider using the V-rescale thermostat.
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 3 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: The Berendsen thermostat does not generate the correct kinetic energy
43: distribution. You might want to consider using the V-rescale thermostat.
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.471 0.236 199.8
43: (ns/day) (hour/ns)
43: Performance: 6.236 3.849
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.290 0.146 198.8
43: (ns/day) (hour/ns)
43: Performance: 5.324 4.508
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.466 0.233 199.7
43: (ns/day) (hour/ns)
43: Performance: 3.335 7.195
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (700 ms)
43: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: The Berendsen thermostat does not generate the correct kinetic energy
43: distribution. You might want to consider using the V-rescale thermostat.
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 3 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
43: The Berendsen thermostat does not generate the correct kinetic energy
43: distribution. You might want to consider using the V-rescale thermostat.
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.384 0.192 199.7
43: (ns/day) (hour/ns)
43: Performance: 7.637 3.142
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.290 0.145 199.5
43: (ns/day) (hour/ns)
43: Performance: 5.349 4.487
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.311 0.156 199.6
43: (ns/day) (hour/ns)
43: Performance: 4.984 4.815
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (577 ms)
43: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.474 0.237 199.8
43: (ns/day) (hour/ns)
43: Performance: 6.189 3.878
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.290 0.145 199.5
43: (ns/day) (hour/ns)
43: Performance: 5.350 4.486
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.490 0.245 199.8
43: (ns/day) (hour/ns)
43: Performance: 3.174 7.562
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (711 ms)
43: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.296 0.148 199.6
43: (ns/day) (hour/ns)
43: Performance: 9.900 2.424
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.512 0.257 199.7
43: (ns/day) (hour/ns)
43: Performance: 3.031 7.919
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.289 0.145 199.5
43: (ns/day) (hour/ns)
43: Performance: 5.361 4.476
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (634 ms)
43: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
43: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
43:
43:
43: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
43: Using Berendsen pressure coupling invalidates the true ensemble for the
43: thermostat
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 3 notes
43:
43: There was 1 warning
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
43: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
43:
43:
43: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
43: Using Berendsen pressure coupling invalidates the true ensemble for the
43: thermostat
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 3 notes
43:
43: There was 1 warning
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.539 0.270 199.8
43: (ns/day) (hour/ns)
43: Performance: 5.446 4.407
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.290 0.146 199.5
43: (ns/day) (hour/ns)
43: Performance: 5.343 4.492
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.489 0.245 199.8
43: (ns/day) (hour/ns)
43: Performance: 3.174 7.562
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (744 ms)
43: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
43: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 3 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
43: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.496 0.248 199.8
43: (ns/day) (hour/ns)
43: Performance: 5.921 4.053
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.291 0.146 199.5
43: (ns/day) (hour/ns)
43: Performance: 5.338 4.496
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.512 0.256 199.8
43: (ns/day) (hour/ns)
43: Performance: 3.037 7.902
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (734 ms)
43: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
43: The Berendsen thermostat does not generate the correct kinetic energy
43: distribution. You might want to consider using the V-rescale thermostat.
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 3 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
43: The Berendsen thermostat does not generate the correct kinetic energy
43: distribution. You might want to consider using the V-rescale thermostat.
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.495 0.248 199.8
43: (ns/day) (hour/ns)
43: Performance: 5.924 4.051
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.290 0.145 199.5
43: (ns/day) (hour/ns)
43: Performance: 5.352 4.484
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.534 0.267 199.8
43: (ns/day) (hour/ns)
43: Performance: 2.911 8.245
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (744 ms)
43: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7
43: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (0 ms)
43: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/8
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.451 0.226 199.8
43: (ns/day) (hour/ns)
43: Performance: 6.509 3.687
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.490 0.246 199.7
43: (ns/day) (hour/ns)
43: Performance: 3.167 7.578
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.511 0.256 199.8
43: (ns/day) (hour/ns)
43: Performance: 3.040 7.895
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_secondpart.part0002.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/8 (810 ms)
43: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/9
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.675 0.338 199.9
43: (ns/day) (hour/ns)
43: Performance: 4.352 5.515
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.469 0.235 199.8
43: (ns/day) (hour/ns)
43: Performance: 3.311 7.247
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.623 0.312 199.9
43: (ns/day) (hour/ns)
43: Performance: 2.493 9.626
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_secondpart.part0002.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/9 (968 ms)
43: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/10
43: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/10 (0 ms)
43: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/11
43: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/11 (1 ms)
43: [----------] 12 tests from NPT/MdrunNoAppendContinuationIsExact (6624 ms total)
43:
43: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact
43: [ RUN ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.336 0.168 199.7
43: (ns/day) (hour/ns)
43: Performance: 8.725 2.751
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 8 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.402 0.202 199.6
43: (ns/day) (hour/ns)
43: Performance: 3.857 6.223
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.643 0.322 199.8
43: (ns/day) (hour/ns)
43: Performance: 2.418 9.924
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (787 ms)
43: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact (787 ms total)
43:
43: [----------] 3 tests from Checking/InitialConstraintsTest
43: [ RUN ] Checking/InitialConstraintsTest.Works/0
43: Setting the LD random seed to -1153604830
43: Generated 8 of the 10 non-bonded parameter combinations
43: Excluding 2 bonded neighbours molecule type 'Methanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group rest is 11.00
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]:
43: NVE simulation: will use the initial temperature of 1141.954 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc-and-methanol'
43: 1 steps, 0.0 ps.
43: turning H bonds into constraints...
43: turning H bonds into constraints...
43: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K
43: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.266 0.133 199.6
43: (ns/day) (hour/ns)
43: Performance: 1.297 18.502
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_spc-and-methanol.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/0 (173 ms)
43: [ RUN ] Checking/InitialConstraintsTest.Works/1
43: Setting the LD random seed to 1238903015
43: Generated 8 of the 10 non-bonded parameter combinations
43: Excluding 2 bonded neighbours molecule type 'Methanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group rest is 11.00
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]:
43: NVE simulation: will use the initial temperature of 1141.954 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc-and-methanol'
43: 1 steps, 0.0 ps.
43: turning H bonds into constraints...
43: turning H bonds into constraints...
43: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K
43: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.431 0.216 199.8
43: (ns/day) (hour/ns)
43: Performance: 0.801 29.959
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_spc-and-methanol.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/1 (256 ms)
43: [ RUN ] Checking/InitialConstraintsTest.Works/2
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]:
43: Integrator method md-vv-avek is implemented primarily for validation
43: purposes; for molecular dynamics, you should probably be using md or md-vv
43:
43: Setting the LD random seed to 1259045145
43: Generated 8 of the 10 non-bonded parameter combinations
43: Excluding 2 bonded neighbours molecule type 'Methanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group rest is 11.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]:
43: NVE simulation: will use the initial temperature of 1141.954 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc-and-methanol'
43: 1 steps, 0.0 ps.
43: turning H bonds into constraints...
43: turning H bonds into constraints...
43: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K
43: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.245 0.123 199.5
43: (ns/day) (hour/ns)
43: Performance: 1.407 17.061
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_spc-and-methanol.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/2 (167 ms)
43: [----------] 3 tests from Checking/InitialConstraintsTest (597 ms total)
43:
43: [----------] 2 tests from WithIntegrator/ImdTest
43: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/0
43: Setting the LD random seed to -637732963
43: Generated 20503 of the 20503 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 1
43: Generated 17396 of the 20503 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'Glycine'
43:
43: NOTE 1 [file glycine_vacuo.top, line 12]:
43: The bond in molecule-type Glycine between atoms 1 N and 2 H1 has an
43: estimated oscillational period of 1.0e-02 ps, which is less than 10 times
43: the time step of 2.0e-03 ps.
43: Maybe you forgot to change the constraints mdp option.
43:
43: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD).
43: Number of degrees of freedom in T-Coupling group System is 27.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 10 to 50, rlist from 1.026 to 1.34
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43:
43: IMD: Enabled. This simulation will accept incoming IMD connections.
43: IMD: Pulling from IMD remote is enabled (-imdpull).
43: IMD: Setting port for connection requests to 0.
43: IMD: Setting up incoming socket.
43: IMD: Listening for IMD connection on port 43127.
43: IMD: -imdwait not set, starting simulation.
43: starting mdrun 'Glycine'
43: 2 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
43: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.026 nm, buffer size 0.026 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.438 0.219 199.7
43: (ns/day) (hour/ns)
43: Performance: 2.365 10.149
43: [ OK ] WithIntegrator/ImdTest.ImdCanRun/0 (1331 ms)
43: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/1
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]:
43: Setting tcoupl from 'V-rescale' to 'no'. Temperature coupling does not
43: apply to steep.
43:
43: Setting the LD random seed to -1281122796
43: Generated 20503 of the 20503 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 1
43: Generated 17396 of the 20503 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'Glycine'
43: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD).
43: Number of degrees of freedom in T-Coupling group System is 27.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43:
43: IMD: Enabled. This simulation will accept incoming IMD connections.
43: IMD: Pulling from IMD remote is enabled (-imdpull).
43: IMD: Setting port for connection requests to 0.
43: IMD: Setting up incoming socket.
43: IMD: Listening for IMD connection on port 43221.
43: IMD: -imdwait not set, starting simulation.
43:
43: Steepest Descents:
43: Tolerance (Fmax) = 1.00000e+01
43: Number of steps = 2
43:
43: Energy minimization reached the maximum number of steps before the forces
43: reached the requested precision Fmax < 10.
43:
43: writing lowest energy coordinates.
43:
43: Steepest Descents did not converge to Fmax < 10 in 3 steps.
43: Potential Energy = 1.19770464690297e+03
43: Maximum force = 1.77948604657896e+04 on atom 9
43: Norm of force = 7.87328617833980e+03
43: This run will generate roughly 0 Mb of data
43: [ OK ] WithIntegrator/ImdTest.ImdCanRun/1 (1105 ms)
43: [----------] 2 tests from WithIntegrator/ImdTest (2436 ms total)
43:
43: [----------] 2 tests from Argon12/OutputFiles
43: [ RUN ] Argon12/OutputFiles.FilesArePresent/0
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]:
43: NVE simulation: will use the initial temperature of 68.810 K for
43: determining the Verlet buffer size
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.498 0.249 199.8
43: (ns/day) (hour/ns)
43: Performance: 5.891 4.074
43: [ OK ] Argon12/OutputFiles.FilesArePresent/0 (285 ms)
43: [ RUN ] Argon12/OutputFiles.FilesArePresent/1
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]:
43: NVE simulation: will use the initial temperature of 68.810 K for
43: determining the Verlet buffer size
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.329 0.165 199.8
43: (ns/day) (hour/ns)
43: Performance: 8.917 2.692
43: [ OK ] Argon12/OutputFiles.FilesArePresent/1 (200 ms)
43: [----------] 2 tests from Argon12/OutputFiles (485 ms total)
43:
43: [----------] 4 tests from SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest
43: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/0
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_0_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_0_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_0_input.mdp]:
43: NVE simulation: will use the initial temperature of 68.810 K for
43: determining the Verlet buffer size
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.528 0.264 199.9
43: (ns/day) (hour/ns)
43: Performance: 5.562 4.315
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.316 0.158 199.7
43: (ns/day) (hour/ns)
43: Performance: 9.293 2.583
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016 trr version: GMX_trn_file (double precision)
43:
43:
43: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/0 (480 ms)
43: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/1
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.456 0.228 199.9
43: (ns/day) (hour/ns)
43: Performance: 6.435 3.730
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.292 0.146 199.7
43: (ns/day) (hour/ns)
43: Performance: 10.037 2.391
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
43:
43: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/1 (434 ms)
43: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/2
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 330891 of the 330891 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 330891 of the 330891 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 27.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_input.mdp]:
43: NVE simulation: will use the initial temperature of 398.997 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 4 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
43: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.463 0.231 199.9
43: (ns/day) (hour/ns)
43: Performance: 6.347 3.781
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 16 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.278 0.139 199.6
43: (ns/day) (hour/ns)
43: Performance: 10.564 2.272
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_sim1.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_sim2.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
43:
43: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/2 (4613 ms)
43: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/3
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_3_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_3_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 330891 of the 330891 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 330891 of the 330891 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 27.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_3_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_3_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.435 0.218 199.9
43: (ns/day) (hour/ns)
43: Performance: 6.744 3.559
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_3_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 16 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.254 0.127 199.6
43: (ns/day) (hour/ns)
43: Performance: 11.559 2.076
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_3_sim1.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_3_sim2.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
43:
43: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/3 (4578 ms)
43: [----------] 4 tests from SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest (10105 ms total)
43:
43: [----------] 8 tests from SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest
43: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/0
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_input.mdp]:
43: NVE simulation: will use the initial temperature of 68.810 K for
43: determining the Verlet buffer size
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.554 0.277 199.8
43: (ns/day) (hour/ns)
43: Performance: 5.299 4.529
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.353 0.177 199.8
43: (ns/day) (hour/ns)
43: Performance: 8.317 2.886
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
43:
43: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/0 (520 ms)
43: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/1
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_input.mdp]:
43: NVE simulation: will use the initial temperature of 68.810 K for
43: determining the Verlet buffer size
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.579 0.290 199.8
43: (ns/day) (hour/ns)
43: Performance: 5.069 4.735
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.531 0.266 199.9
43: (ns/day) (hour/ns)
43: Performance: 5.525 4.344
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
43:
43: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/1 (621 ms)
43: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/2
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.337 0.169 199.7
43: (ns/day) (hour/ns)
43: Performance: 8.710 2.755
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.488 0.244 199.9
43: (ns/day) (hour/ns)
43: Performance: 6.011 3.993
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_sim1.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_sim2.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
43:
43: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/2 (479 ms)
43: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/3
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_3_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_3_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group System is 33.00
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_3_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
43: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.333 0.167 199.7
43: (ns/day) (hour/ns)
43: Performance: 8.821 2.721
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_3_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 16 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.466 0.233 199.8
43: (ns/day) (hour/ns)
43: Performance: 6.295 3.813
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_3_sim1.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_3_sim2.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
43:
43: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/3 (465 ms)
43: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/4
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 330891 of the 330891 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 330891 of the 330891 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 27.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_input.mdp]:
43: NVE simulation: will use the initial temperature of 398.997 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 4 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
43: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.490 0.245 199.8
43: (ns/day) (hour/ns)
43: Performance: 5.990 4.007
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 16 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.330 0.165 199.8
43: (ns/day) (hour/ns)
43: Performance: 8.906 2.695
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_sim1.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_sim2.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
43:
43: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/4 (4602 ms)
43: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/5
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 330891 of the 330891 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 330891 of the 330891 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 27.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_input.mdp]:
43: NVE simulation: will use the initial temperature of 398.997 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 4 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
43: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.587 0.294 199.8
43: (ns/day) (hour/ns)
43: Performance: 5.003 4.797
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 16 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.595 0.298 199.7
43: (ns/day) (hour/ns)
43: Performance: 4.932 4.866
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_sim1.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_sim2.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
43:
43: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/5 (4791 ms)
43: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/6
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 330891 of the 330891 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 330891 of the 330891 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 27.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.515 0.258 199.8
43: (ns/day) (hour/ns)
43: Performance: 5.700 4.210
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 16 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.369 0.184 199.8
43: (ns/day) (hour/ns)
43: Performance: 7.962 3.014
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_sim1.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_sim2.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
43:
43: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/6 (4672 ms)
43: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/7
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_input.mdp]:
43: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
43: that with the Verlet scheme, nstlist has no effect on the accuracy of
43: your simulation.
43:
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (4)
43:
43: Generated 330891 of the 330891 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 330891 of the 330891 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 27.00
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 16 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
43: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.571 0.286 199.8
43: (ns/day) (hour/ns)
43: Performance: 5.142 4.668
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc2'
43: 16 steps, 0.0 ps.
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.345 0.173 199.8
43: (ns/day) (hour/ns)
43: Performance: 8.497 2.825
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_sim1.edr as double precision energy file
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_sim2.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
43:
43: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/7 (4670 ms)
43: [----------] 8 tests from SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest (20825 ms total)
43:
43: [----------] 3 tests from MdrunCanWrite/Trajectories
43: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0
43: Setting the LD random seed to 130678708
43: Generated 8 of the 10 non-bonded parameter combinations
43: Excluding 2 bonded neighbours molecule type 'Methanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 12.00
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There was 1 note
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc-and-methanol'
43: 6 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.284 0.142 199.6
43: (ns/day) (hour/ns)
43: Performance: 4.257 5.637
43: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 (194 ms)
43: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1
43: Setting the LD random seed to 1475850147
43: Generated 8 of the 10 non-bonded parameter combinations
43: Excluding 2 bonded neighbours molecule type 'Methanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 12.00
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There was 1 note
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc-and-methanol'
43: 6 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.249 0.125 199.5
43: (ns/day) (hour/ns)
43: Performance: 4.852 4.946
43: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 (177 ms)
43: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2
43: Setting the LD random seed to -656501414
43: Generated 8 of the 10 non-bonded parameter combinations
43: Excluding 2 bonded neighbours molecule type 'Methanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 12.00
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There was 1 note
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc-and-methanol'
43: 6 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.382 0.191 199.7
43: (ns/day) (hour/ns)
43: Performance: 3.164 7.586
43: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 (244 ms)
43: [----------] 3 tests from MdrunCanWrite/Trajectories (618 ms total)
43:
43: [----------] 3 tests from MdrunCanWrite/NptTrajectories
43: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0
43: Setting the LD random seed to -2048260507
43: Generated 8 of the 10 non-bonded parameter combinations
43: Excluding 2 bonded neighbours molecule type 'Methanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 12.00
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There was 1 note
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc-and-methanol'
43: 2 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.272 0.136 199.6
43: (ns/day) (hour/ns)
43: Performance: 1.900 12.629
43: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 (187 ms)
43: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1
43: Setting the LD random seed to -313100929
43: Generated 8 of the 10 non-bonded parameter combinations
43: Excluding 2 bonded neighbours molecule type 'Methanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 12.00
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There was 1 note
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc-and-methanol'
43: 2 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.430 0.215 199.7
43: (ns/day) (hour/ns)
43: Performance: 1.204 19.928
43: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 (266 ms)
43: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2
43: Setting the LD random seed to 561137923
43: Generated 8 of the 10 non-bonded parameter combinations
43: Excluding 2 bonded neighbours molecule type 'Methanol'
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group System is 12.00
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There was 1 note
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
43: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
43:
43: Using 1 MPI thread
43:
43: Non-default thread affinity set, disabling internal thread affinity
43:
43: Using 2 OpenMP threads
43:
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'spc-and-methanol'
43: 2 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
43: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.252 0.126 199.5
43: (ns/day) (hour/ns)
43: Performance: 2.054 11.684
43: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 (177 ms)
43: [----------] 3 tests from MdrunCanWrite/NptTrajectories (632 ms total)
43:
43: [----------] Global test environment tear-down
43: [==========] 96 tests from 23 test cases ran. (81275 ms total)
43: [ PASSED ] 96 tests.
43/52 Test #43: MdrunTests .......................... Passed 81.41 sec
test 44
Start 44: MdrunNonIntegratorTests
44: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrun-non-integrator-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunNonIntegratorTests.xml"
44: Test timeout computed to be: 600
44: [==========] Running 65 tests from 7 test cases.
44: [----------] Global test environment set-up.
44: [----------] 1 test from NonbondedBenchTest
44: [ RUN ] NonbondedBenchTest.BasicEndToEndTest
44: System size: 3000 atoms
44: Cut-off radius: 1 nm
44: Number of threads: 1
44: Number of iterations: 1
44: Compute energies: no
44: Ewald excl. corr.: analytical
44:
44: Coulomb LJ comb. SIMD Mcycles Mcycles/it. pairs/cycle
44: total useful
44: Ewald all geom. no 0.000 0.0000 inf inf
44: [ OK ] NonbondedBenchTest.BasicEndToEndTest (670 ms)
44: [----------] 1 test from NonbondedBenchTest (670 ms total)
44:
44: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest
44: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
44: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
44: nstcomm to nstcalcenergy
44:
44: Generated 330891 of the 330891 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 330891 of the 330891 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 27.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44:
44: Steepest Descents:
44: Tolerance (Fmax) = 1.00000e+01
44: Number of steps = 4
44:
44: Energy minimization reached the maximum number of steps before the forces
44: reached the requested precision Fmax < 10.
44:
44: writing lowest energy coordinates.
44:
44: Steepest Descents did not converge to Fmax < 10 in 5 steps.
44: Potential Energy = -4.79910463671071e+01
44: Maximum force = 1.86297359432220e+02 on atom 13
44: Norm of force = 8.77219865482161e+01
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 This run will generate roughly 0 Mb of data
44: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (4127 ms)
44: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
44: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
44: nstcomm to nstcalcenergy
44:
44: Generated 330891 of the 330891 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 330891 of the 330891 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 27.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44:
44: Polak-Ribiere Conjugate Gradients:
44: Tolerance (Fmax) = 1.00000e+01
44: Number of steps = 4
44: F-max = 3.02331e+02 on atom 3
44: F-Norm = 1.18024e+02
44:
44:
44: Energy minimization reached the maximum number of steps before the forces
44: reached the requested precision Fmax < 10.
44:
44: writing lowest energy coordinates.
44:
44: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
44: Potential Energy = -5.58622538633290e+01
44: Maximum force = 4.27274822366523e+02 on atom 13
44: Norm of force = 1.84530029253828e+02
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data
44: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (4134 ms)
44: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
44: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
44: nstcomm to nstcalcenergy
44:
44: Generated 20503 of the 20503 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 1
44: Generated 17396 of the 20503 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Glycine'
44: Number of degrees of freedom in T-Coupling group System is 22.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44:
44: Steepest Descents:
44: Tolerance (Fmax) = 1.00000e+01
44: Number of steps = 4
44:
44: Energy minimization reached the maximum number of steps before the forces
44: reached the requested precision Fmax < 10.
44:
44: writing lowest energy coordinates.
44:
44: Steepest Descents did not converge to Fmax < 10 in 5 steps.
44: Potential Energy = 3.19376899751521e+02
44: Maximum force = 9.99884921009767e+03 on atom 9
44: Norm of force = 4.61669565054298e+03
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 turning H bonds into constraints...
44: This run will generate roughly 0 Mb of data
44: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (1068 ms)
44: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
44: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
44: nstcomm to nstcalcenergy
44:
44: Generated 20503 of the 20503 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 1
44: Generated 17396 of the 20503 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Glycine'
44:
44: NOTE 3 [file glycine_vacuo.top, line 12]:
44: For accurate cg with LINCS constraints, lincs-order should be 8 or more.
44:
44: Number of degrees of freedom in T-Coupling group System is 22.00
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44:
44: Polak-Ribiere Conjugate Gradients:
44: Tolerance (Fmax) = 1.00000e+01
44: Number of steps = 4
44: F-max = 2.41575e+04 on atom 10
44: F-Norm = 1.18451e+04
44:
44:
44: Energy minimization reached the maximum number of steps before the forces
44: reached the requested precision Fmax < 10.
44:
44: writing lowest energy coordinates.
44:
44: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
44: Potential Energy = 1.51743018140925e+02
44: Maximum force = 7.42089573409111e+03 on atom 9
44: Norm of force = 3.56929298615739e+03
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 turning H bonds into constraints...
44: This run will generate roughly 0 Mb of data
44: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (1050 ms)
44: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
44: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
44: nstcomm to nstcalcenergy
44:
44: Generated 2145 of the 2145 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2145 of the 2145 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
44:
44: NOTE 3 [file unknown]:
44: You are using constraints on all bonds, whereas the forcefield has been
44: parametrized only with constraints involving hydrogen atoms. We suggest
44: using constraints = h-bonds instead, this will also improve performance.
44:
44: Cleaning up constraints and constant bonded interactions with virtual sites
44: Removed 18 Angles with virtual sites, 21 left
44: Removed 10 Proper Dih.s with virtual sites, 44 left
44: Converted 15 Constraints with virtual sites to connections, 7 left
44: Number of degrees of freedom in T-Coupling group System is 23.00
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44:
44: Steepest Descents:
44: Tolerance (Fmax) = 1.00000e+01
44: Number of steps = 4
44:
44: Energy minimization reached the maximum number of steps before the forces
44: reached the requested precision Fmax < 10.
44:
44: writing lowest energy coordinates.
44:
44: Steepest Descents did not converge to Fmax < 10 in 5 steps.
44: Potential Energy = -1.56984193848276e+02
44: Maximum force = 4.56923624626296e+02 on atom 17
44: Norm of force = 1.83258377168331e+02
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 3.000
Last energy frame read 2 time 3.000 turning all bonds into constraints...
44: This run will generate roughly 0 Mb of data
44: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (127 ms)
44: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
44: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
44: nstcomm to nstcalcenergy
44:
44: Generated 2145 of the 2145 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2145 of the 2145 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
44:
44: NOTE 3 [file unknown]:
44: You are using constraints on all bonds, whereas the forcefield has been
44: parametrized only with constraints involving hydrogen atoms. We suggest
44: using constraints = h-bonds instead, this will also improve performance.
44:
44:
44: NOTE 4 [file unknown]:
44: For accurate cg with LINCS constraints, lincs-order should be 8 or more.
44:
44: Cleaning up constraints and constant bonded interactions with virtual sites
44: Removed 18 Angles with virtual sites, 21 left
44: Removed 10 Proper Dih.s with virtual sites, 44 left
44: Converted 15 Constraints with virtual sites to connections, 7 left
44: Number of degrees of freedom in T-Coupling group System is 23.00
44:
44: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 5 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44:
44: Polak-Ribiere Conjugate Gradients:
44: Tolerance (Fmax) = 1.00000e+01
44: Number of steps = 4
44: F-max = 1.06800e+03 on atom 28
44: F-Norm = 4.26922e+02
44:
44:
44: Energy minimization reached the maximum number of steps before the forces
44: reached the requested precision Fmax < 10.
44:
44: writing lowest energy coordinates.
44:
44: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
44: Potential Energy = -1.69410778678185e+02
44: Maximum force = 2.18225948473957e+02 on atom 17
44: Norm of force = 7.92068036537697e+01
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 turning all bonds into constraints...
44: This run will generate roughly 0 Mb of data
44: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (128 ms)
44: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (10634 ms total)
44:
44: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest
44: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
44: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
44: nstcomm to nstcalcenergy
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44:
44: Steepest Descents:
44: Tolerance (Fmax) = 1.00000e+01
44: Number of steps = 4
44:
44: writing lowest energy coordinates.
44:
44: Steepest Descents converged to Fmax < 10 in 1 steps
44: Potential Energy = -9.74257075835450e-01
44: Maximum force = 4.01322929015108e+00 on atom 1
44: Norm of force = 1.63839399694368e+00
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
44: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (36 ms)
44: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
44: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
44: nstcomm to nstcalcenergy
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44:
44: Polak-Ribiere Conjugate Gradients:
44: Tolerance (Fmax) = 1.00000e+01
44: Number of steps = 4
44: F-max = 4.01323e+00 on atom 1
44: F-Norm = 1.63839e+00
44:
44:
44: writing lowest energy coordinates.
44:
44: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps
44: Potential Energy = -9.90642313893957e-01
44: Maximum force = 2.57812909491105e+00 on atom 1
44: Norm of force = 1.05251679559258e+00
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Last energy frame read 1 time 0.000 This run will generate roughly 0 Mb of data
44: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (36 ms)
44: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
44: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
44: nstcomm to nstcalcenergy
44:
44:
44: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
44: For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44:
44: There was 1 warning
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank.
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44:
44: Low-Memory BFGS Minimizer:
44: Tolerance (Fmax) = 1.00000e+01
44: Number of steps = 4
44: Using 10 BFGS correction steps.
44:
44: F-max = 4.01323e+00 on atom 1
44: F-Norm = 1.63839e+00
44:
44:
44: writing lowest energy coordinates.
44:
44: Low-Memory BFGS Minimizer converged to Fmax < 10 in 0 steps
44: Potential Energy = -9.90642313893957e-01
44: Maximum force = 2.57812909491105e+00 on atom 1
44: Norm of force = 1.05251679559258e+00
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Last energy frame read 1 time 0.000 This run will generate roughly 0 Mb of data
44: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (37 ms)
44: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
44: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
44: nstcomm to nstcalcenergy
44:
44: Generated 20503 of the 20503 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 1
44: Generated 17396 of the 20503 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Glycine'
44: Number of degrees of freedom in T-Coupling group System is 27.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44:
44: Steepest Descents:
44: Tolerance (Fmax) = 1.00000e+01
44: Number of steps = 4
44:
44: Energy minimization reached the maximum number of steps before the forces
44: reached the requested precision Fmax < 10.
44:
44: writing lowest energy coordinates.
44:
44: Steepest Descents did not converge to Fmax < 10 in 5 steps.
44: Potential Energy = 3.19395484891517e+02
44: Maximum force = 9.97041707197910e+03 on atom 9
44: Norm of force = 4.62274878665467e+03
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 This run will generate roughly 0 Mb of data
44: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (1065 ms)
44: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
44: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
44: nstcomm to nstcalcenergy
44:
44: Generated 20503 of the 20503 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 1
44: Generated 17396 of the 20503 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Glycine'
44: Number of degrees of freedom in T-Coupling group System is 27.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44:
44: Polak-Ribiere Conjugate Gradients:
44: Tolerance (Fmax) = 1.00000e+01
44: Number of steps = 4
44: F-max = 2.41672e+04 on atom 10
44: F-Norm = 1.19357e+04
44:
44:
44: Energy minimization reached the maximum number of steps before the forces
44: reached the requested precision Fmax < 10.
44:
44: writing lowest energy coordinates.
44:
44: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
44: Potential Energy = 1.56258793899479e+02
44: Maximum force = 7.50181017480397e+03 on atom 9
44: Norm of force = 3.61390332564874e+03
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data
44: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (1064 ms)
44: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
44: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
44: nstcomm to nstcalcenergy
44:
44:
44: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
44: For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
44:
44: Generated 20503 of the 20503 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 1
44: Generated 17396 of the 20503 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Glycine'
44: Number of degrees of freedom in T-Coupling group System is 27.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44:
44: There was 1 warning
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank.
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44:
44: Low-Memory BFGS Minimizer:
44: Tolerance (Fmax) = 1.00000e+01
44: Number of steps = 4
44: Using 10 BFGS correction steps.
44:
44: F-max = 2.41672e+04 on atom 10
44: F-Norm = 1.19357e+04
44:
44:
44: Energy minimization reached the maximum number of steps before the forces
44: reached the requested precision Fmax < 10.
44:
44: writing lowest energy coordinates.
44:
44: Low-Memory BFGS Minimizer did not converge to Fmax < 10 in 5 steps.
44: Potential Energy = 5.61116097794203e+02
44: Maximum force = 1.26854826291223e+04 on atom 10
44: Norm of force = 6.06436286976271e+03
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data
44: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (1080 ms)
44: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (3318 ms total)
44:
44: [----------] 5 tests from NormalModesWorks/NormalModesTest
44: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/0
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0_input.mdp]:
44: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
44: nstcomm to nstcalcenergy
44:
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 15.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44:
44: Small system size (N=6), using full Hessian format.
44: Allocating Hessian memory...
44:
44: starting normal mode calculation '2 scaled waters'
44: 12 steps.
44:
44: Maximum force: 9.96989e-06
44:
44:
44: Writing Hessian...
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Reading double precision matrix generated by GROMACS 2020.3-Raspbian-2020.3-1
44:
44: Diagonalizing to find vectors 7 through 18...
44: Writing eigenvalues...
44:
44: Writing average structure & eigenvectors 7--18 to eigenvec.trr
44: This run will generate roughly 0 Mb of data
44: There are: 6 Atoms
44: Using begin = 7 and end = 18
44: Full matrix storage format, nrow=18, ncols=18
44: Writing eigenfrequencies - negative eigenvalues will be set to zero.
44: Cannot compute entropy when -first = 7
44: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/0 (64 ms)
44: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/1
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1_input.mdp]:
44: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
44: nstcomm to nstcalcenergy
44:
44: Generated 20503 of the 20503 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 1
44: Generated 17396 of the 20503 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
44:
44: NOTE 3 [file villin.top, line 2452]:
44: System has non-zero total charge: -2.000000
44: Total charge should normally be an integer. See
44: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
44: for discussion on how close it should be to an integer.
44:
44:
44:
44: Number of degrees of freedom in T-Coupling group System is 765.00
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44:
44: Small system size (N=256), using full Hessian format.
44: Allocating Hessian memory...
44:
44: starting normal mode calculation 'AMYLOID BETA A4 PROTEIN'
44: 512 steps.
44:
44: Maximum force: 6.97568e-04
44:
44:
44: Writing Hessian...
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Reading double precision matrix generated by GROMACS 2020.3-Raspbian-2020.3-1
44:
44: Diagonalizing to find vectors 7 through 50...
44: Writing eigenvalues...
44:
44: Writing average structure & eigenvectors 7--50 to eigenvec.trr
44: This run will generate roughly 0 Mb of data
44: There are: 256 Atoms
44: Using begin = 7 and end = 50
44: Full matrix storage format, nrow=768, ncols=768
44: Writing eigenfrequencies - negative eigenvalues will be set to zero.
44: Cannot compute entropy when -first = 7
44: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/1 (20724 ms)
44: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/2
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2_input.mdp]:
44: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
44: nstcomm to nstcalcenergy
44:
44: Generated 330891 of the 330891 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 330891 of the 330891 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 15.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44:
44: Small system size (N=6), using full Hessian format.
44: Allocating Hessian memory...
44:
44: starting normal mode calculation 'flex spc dimer'
44: 12 steps.
44:
44: Maximum force: 3.36401e-04
44:
44:
44: Writing Hessian...
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Reading double precision matrix generated by GROMACS 2020.3-Raspbian-2020.3-1
44:
44: Diagonalizing to find vectors 7 through 18...
44: Writing eigenvalues...
44:
44: Writing average structure & eigenvectors 7--18 to eigenvec.trr
44: This run will generate roughly 0 Mb of data
44: There are: 6 Atoms
44: Using begin = 7 and end = 18
44: Full matrix storage format, nrow=18, ncols=18
44: Writing eigenfrequencies - negative eigenvalues will be set to zero.
44: Cannot compute entropy when -first = 7
44: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/2 (4291 ms)
44: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/3
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3_input.mdp]:
44: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
44: nstcomm to nstcalcenergy
44:
44: Generated 330891 of the 330891 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 330891 of the 330891 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Cleaning up constraints and constant bonded interactions with virtual sites
44: Number of degrees of freedom in T-Coupling group System is 6.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44:
44: Small system size (N=3), using full Hessian format.
44: Allocating Hessian memory...
44:
44: starting normal mode calculation '1 TIP5P'
44: 6 steps.
44:
44: Maximum force: 2.42882e-04
44:
44:
44: Writing Hessian...
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Reading double precision matrix generated by GROMACS 2020.3-Raspbian-2020.3-1
44:
44: Diagonalizing to find vectors 7 through 9...
44: Writing eigenvalues...
44:
44: Writing average structure & eigenvectors 7--9 to eigenvec.trr
44: This run will generate roughly 0 Mb of data
44: There are: 3 Atoms
44: There are: 2 VSites
44: Using begin = 7 and end = 9
44: Full matrix storage format, nrow=9, ncols=9
44: Writing eigenfrequencies - negative eigenvalues will be set to zero.
44: Cannot compute entropy when -first = 7
44: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/3 (4156 ms)
44: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/4
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44: Generated 6 of the 10 non-bonded parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SW'
44: Cleaning up constraints and constant bonded interactions with virtual sites
44: Number of degrees of freedom in T-Coupling group System is 15.00
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44:
44: Small system size (N=6), using full Hessian format.
44: Allocating Hessian memory...
44:
44: starting normal mode calculation 'sw dimer'
44: 12 steps.
44:
44: Maximum force: 1.07599e-03
44: The force is probably not small enough to ensure that you are at a minimum.
44: Be aware that negative eigenvalues may occur
44: when the resulting matrix is diagonalized.
44:
44:
44: Writing Hessian...
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Reading double precision matrix generated by GROMACS 2020.3-Raspbian-2020.3-1
44:
44: Diagonalizing to find vectors 7 through 18...
44: Writing eigenvalues...
44:
44: Writing average structure & eigenvectors 7--18 to eigenvec.trr
44: This run will generate roughly 0 Mb of data
44: There are: 6 Atoms
44: There are: 2 Shells
44: There are: 2 VSites
44:
44: NOTE: in the current version shell prediction during the crun is disabled
44:
44: Using begin = 7 and end = 18
44: Full matrix storage format, nrow=18, ncols=18
44: Writing eigenfrequencies - negative eigenvalues will be set to zero.
44: Cannot compute entropy when -first = 7
44: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/4 (99 ms)
44: [----------] 5 tests from NormalModesWorks/NormalModesTest (29337 ms total)
44:
44: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest
44: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]:
44: NVE simulation: will use the initial temperature of 68.810 K for
44: determining the Verlet buffer size
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.344 0.172 199.7
44: (ns/day) (hour/ns)
44: Performance: 8.538 2.811
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun 'Argon', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.trr'
44:
44: trr version: GMX_trn_file (double precision)
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.007 0.003 193.8
44: (ns/day) (hour/ns)
44: Performance: 426.457 0.056
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 (230 ms)
44: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]:
44: NVE simulation: will use the initial temperature of 68.810 K for
44: determining the Verlet buffer size
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.323 0.162 199.6
44: (ns/day) (hour/ns)
44: Performance: 9.077 2.644
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun 'Argon', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.009 0.005 195.3
44: (ns/day) (hour/ns)
44: Performance: 314.252 0.076
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 (230 ms)
44: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.708 nm, buffer size 0.008 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.708 nm, buffer size 0.008 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.325 0.163 199.7
44: (ns/day) (hour/ns)
44: Performance: 9.024 2.659
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun 'Argon', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.008 0.004 194.7
44: (ns/day) (hour/ns)
44: Performance: 380.495 0.063
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 (232 ms)
44: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.327 0.164 199.7
44: (ns/day) (hour/ns)
44: Performance: 8.969 2.676
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun 'Argon', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.008 0.004 194.8
44: (ns/day) (hour/ns)
44: Performance: 375.715 0.064
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 (233 ms)
44: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 330891 of the 330891 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 330891 of the 330891 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 27.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]:
44: NVE simulation: will use the initial temperature of 398.997 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
44: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.356 0.179 199.6
44: (ns/day) (hour/ns)
44: Performance: 8.226 2.918
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun 'spc2', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.008 0.004 194.8
44: (ns/day) (hour/ns)
44: Performance: 350.671 0.068
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 (4336 ms)
44: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 330891 of the 330891 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 330891 of the 330891 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 27.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]:
44: NVE simulation: will use the initial temperature of 398.997 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
44: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.387 0.194 199.9
44: (ns/day) (hour/ns)
44: Performance: 7.576 3.168
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun 'spc2', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.008 0.004 194.4
44: (ns/day) (hour/ns)
44: Performance: 354.444 0.068
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 (4364 ms)
44: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 330891 of the 330891 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 330891 of the 330891 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 27.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.733 to 0.824
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.735 nm, buffer size 0.035 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.733 nm, buffer size 0.033 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.453 0.227 199.8
44: (ns/day) (hour/ns)
44: Performance: 6.474 3.707
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.733 to 0.824
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun 'spc2', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.008 0.004 194.0
44: (ns/day) (hour/ns)
44: Performance: 376.956 0.064
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 (4375 ms)
44: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 330891 of the 330891 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 330891 of the 330891 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 27.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.406 0.203 199.7
44: (ns/day) (hour/ns)
44: Performance: 7.234 3.318
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun 'spc2', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.008 0.004 194.1
44: (ns/day) (hour/ns)
44: Performance: 360.543 0.067
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 (4367 ms)
44: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2145 of the 2145 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2145 of the 2145 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
44:
44: NOTE 3 [file unknown]:
44: You are using constraints on all bonds, whereas the forcefield has been
44: parametrized only with constraints involving hydrogen atoms. We suggest
44: using constraints = h-bonds instead, this will also improve performance.
44:
44: Cleaning up constraints and constant bonded interactions with virtual sites
44: Removed 18 Angles with virtual sites, 21 left
44: Removed 10 Proper Dih.s with virtual sites, 44 left
44: Converted 15 Constraints with virtual sites to connections, 7 left
44: Number of degrees of freedom in T-Coupling group System is 23.00
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
44: NVE simulation: will use the initial temperature of 456.887 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
44: There are 9 non-linear virtual site constructions. Their contribution to
44: the energy error is approximated. In most cases this does not affect the
44: error significantly.
44:
44:
44: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 6 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 16 steps, 0.0 ps.
44: turning all bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
44: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.398 0.199 199.6
44: (ns/day) (hour/ns)
44: Performance: 7.368 3.257
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.014 0.007 195.4
44: (ns/day) (hour/ns)
44: Performance: 200.553 0.120
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 (390 ms)
44: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2145 of the 2145 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2145 of the 2145 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
44:
44: NOTE 3 [file unknown]:
44: You are using constraints on all bonds, whereas the forcefield has been
44: parametrized only with constraints involving hydrogen atoms. We suggest
44: using constraints = h-bonds instead, this will also improve performance.
44:
44: Cleaning up constraints and constant bonded interactions with virtual sites
44: Removed 18 Angles with virtual sites, 21 left
44: Removed 10 Proper Dih.s with virtual sites, 44 left
44: Converted 15 Constraints with virtual sites to connections, 7 left
44: Number of degrees of freedom in T-Coupling group System is 23.00
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
44: NVE simulation: will use the initial temperature of 456.887 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
44: There are 9 non-linear virtual site constructions. Their contribution to
44: the energy error is approximated. In most cases this does not affect the
44: error significantly.
44:
44:
44: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 6 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 16 steps, 0.0 ps.
44: turning all bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
44: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.418 0.209 199.7
44: (ns/day) (hour/ns)
44: Performance: 7.020 3.419
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.015 0.008 195.3
44: (ns/day) (hour/ns)
44: Performance: 195.711 0.123
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 (401 ms)
44: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2145 of the 2145 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2145 of the 2145 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
44:
44: NOTE 3 [file unknown]:
44: You are using constraints on all bonds, whereas the forcefield has been
44: parametrized only with constraints involving hydrogen atoms. We suggest
44: using constraints = h-bonds instead, this will also improve performance.
44:
44: Cleaning up constraints and constant bonded interactions with virtual sites
44: Removed 18 Angles with virtual sites, 21 left
44: Removed 10 Proper Dih.s with virtual sites, 44 left
44: Converted 15 Constraints with virtual sites to connections, 7 left
44: Number of degrees of freedom in T-Coupling group System is 23.00
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]:
44: There are 9 non-linear virtual site constructions. Their contribution to
44: the energy error is approximated. In most cases this does not affect the
44: error significantly.
44:
44:
44: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 5 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 16 steps, 0.0 ps.
44: turning all bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.748 nm, buffer size 0.048 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.744 nm, buffer size 0.044 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.380 0.190 199.6
44: (ns/day) (hour/ns)
44: Performance: 7.721 3.109
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.015 0.007 195.4
44: (ns/day) (hour/ns)
44: Performance: 196.491 0.122
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 (528 ms)
44: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2145 of the 2145 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2145 of the 2145 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
44:
44: NOTE 3 [file unknown]:
44: You are using constraints on all bonds, whereas the forcefield has been
44: parametrized only with constraints involving hydrogen atoms. We suggest
44: using constraints = h-bonds instead, this will also improve performance.
44:
44: Cleaning up constraints and constant bonded interactions with virtual sites
44: Removed 18 Angles with virtual sites, 21 left
44: Removed 10 Proper Dih.s with virtual sites, 44 left
44: Converted 15 Constraints with virtual sites to connections, 7 left
44: Number of degrees of freedom in T-Coupling group System is 23.00
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]:
44: There are 9 non-linear virtual site constructions. Their contribution to
44: the energy error is approximated. In most cases this does not affect the
44: error significantly.
44:
44:
44: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 5 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 16 steps, 0.0 ps.
44: turning all bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.432 0.216 199.7
44: (ns/day) (hour/ns)
44: Performance: 6.787 3.536
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.014 0.007 194.2
44: (ns/day) (hour/ns)
44: Performance: 207.686 0.116
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 (494 ms)
44: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest (20183 ms total)
44:
44: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.479 0.240 199.6
44: (ns/day) (hour/ns)
44: Performance: 6.119 3.922
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.018 0.009 190.3
44: (ns/day) (hour/ns)
44: Performance: 159.156 0.151
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 (423 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.433 0.217 199.6
44: (ns/day) (hour/ns)
44: Performance: 6.776 3.542
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.017 0.009 190.4
44: (ns/day) (hour/ns)
44: Performance: 161.200 0.149
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 (400 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.457 0.229 199.6
44: (ns/day) (hour/ns)
44: Performance: 6.417 3.740
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.018 0.009 188.5
44: (ns/day) (hour/ns)
44: Performance: 157.984 0.152
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 (412 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.433 0.217 199.6
44: (ns/day) (hour/ns)
44: Performance: 6.766 3.547
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.017 0.009 188.3
44: (ns/day) (hour/ns)
44: Performance: 158.509 0.151
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 (400 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.455 0.228 199.6
44: (ns/day) (hour/ns)
44: Performance: 6.441 3.726
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.018 0.009 188.5
44: (ns/day) (hour/ns)
44: Performance: 155.567 0.154
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 (411 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.433 0.217 199.6
44: (ns/day) (hour/ns)
44: Performance: 6.763 3.549
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.018 0.009 188.4
44: (ns/day) (hour/ns)
44: Performance: 156.810 0.153
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 (400 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.455 0.228 199.6
44: (ns/day) (hour/ns)
44: Performance: 6.447 3.723
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.017 0.009 187.4
44: (ns/day) (hour/ns)
44: Performance: 158.827 0.151
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 (411 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.500 0.251 199.7
44: (ns/day) (hour/ns)
44: Performance: 5.860 4.096
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.017 0.009 188.3
44: (ns/day) (hour/ns)
44: Performance: 158.786 0.151
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 (433 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.500 0.250 199.7
44: (ns/day) (hour/ns)
44: Performance: 5.870 4.089
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.017 0.009 188.2
44: (ns/day) (hour/ns)
44: Performance: 158.252 0.152
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 (434 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.455 0.228 199.6
44: (ns/day) (hour/ns)
44: Performance: 6.440 3.727
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.017 0.009 188.3
44: (ns/day) (hour/ns)
44: Performance: 158.301 0.152
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 (411 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.455 0.228 199.6
44: (ns/day) (hour/ns)
44: Performance: 6.448 3.722
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.017 0.009 189.6
44: (ns/day) (hour/ns)
44: Performance: 159.225 0.151
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 (412 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.456 0.228 199.8
44: (ns/day) (hour/ns)
44: Performance: 6.434 3.730
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.017 0.009 190.5
44: (ns/day) (hour/ns)
44: Performance: 160.566 0.149
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 (411 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.455 0.228 199.8
44: (ns/day) (hour/ns)
44: Performance: 6.446 3.723
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.018 0.009 190.4
44: (ns/day) (hour/ns)
44: Performance: 159.771 0.150
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 (411 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.433 0.217 199.8
44: (ns/day) (hour/ns)
44: Performance: 6.774 3.543
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.017 0.009 188.3
44: (ns/day) (hour/ns)
44: Performance: 158.073 0.152
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 (400 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.455 0.227 199.8
44: (ns/day) (hour/ns)
44: Performance: 6.456 3.717
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.017 0.009 188.4
44: (ns/day) (hour/ns)
44: Performance: 158.228 0.152
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 (411 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.433 0.217 199.8
44: (ns/day) (hour/ns)
44: Performance: 6.784 3.538
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.017 0.009 188.1
44: (ns/day) (hour/ns)
44: Performance: 158.325 0.152
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 (400 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.433 0.216 199.8
44: (ns/day) (hour/ns)
44: Performance: 6.786 3.537
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.018 0.009 188.4
44: (ns/day) (hour/ns)
44: Performance: 155.913 0.154
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 (401 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.432 0.216 199.8
44: (ns/day) (hour/ns)
44: Performance: 6.793 3.533
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.017 0.009 188.4
44: (ns/day) (hour/ns)
44: Performance: 158.232 0.152
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 (399 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.410 0.205 199.8
44: (ns/day) (hour/ns)
44: Performance: 7.156 3.354
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.017 0.009 188.4
44: (ns/day) (hour/ns)
44: Performance: 158.623 0.151
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 (389 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.455 0.228 199.8
44: (ns/day) (hour/ns)
44: Performance: 6.451 3.721
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.017 0.009 188.4
44: (ns/day) (hour/ns)
44: Performance: 158.236 0.152
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 (411 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.477 0.239 199.8
44: (ns/day) (hour/ns)
44: Performance: 6.153 3.901
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.017 0.009 188.4
44: (ns/day) (hour/ns)
44: Performance: 158.930 0.151
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 (423 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.455 0.228 199.8
44: (ns/day) (hour/ns)
44: Performance: 6.454 3.718
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.018 0.009 188.2
44: (ns/day) (hour/ns)
44: Performance: 157.649 0.152
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 (411 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.461 0.231 199.6
44: (ns/day) (hour/ns)
44: Performance: 6.355 3.776
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.018 0.009 190.7
44: (ns/day) (hour/ns)
44: Performance: 157.262 0.153
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 (526 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.491 0.246 199.6
44: (ns/day) (hour/ns)
44: Performance: 5.969 4.021
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.019 0.010 190.1
44: (ns/day) (hour/ns)
44: Performance: 148.495 0.162
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 (540 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.457 0.229 199.6
44: (ns/day) (hour/ns)
44: Performance: 6.418 3.740
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.018 0.009 188.4
44: (ns/day) (hour/ns)
44: Performance: 155.803 0.154
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 (521 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.438 0.219 199.6
44: (ns/day) (hour/ns)
44: Performance: 6.700 3.582
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.018 0.009 188.3
44: (ns/day) (hour/ns)
44: Performance: 155.822 0.154
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 (511 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 1.398 0.699 199.9
44: (ns/day) (hour/ns)
44: Performance: 2.100 11.429
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.018 0.009 188.5
44: (ns/day) (hour/ns)
44: Performance: 157.524 0.152
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 (992 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.631 0.316 199.7
44: (ns/day) (hour/ns)
44: Performance: 4.651 5.160
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.017 0.009 188.2
44: (ns/day) (hour/ns)
44: Performance: 157.960 0.152
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 (608 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.637 0.319 199.7
44: (ns/day) (hour/ns)
44: Performance: 4.602 5.215
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.018 0.009 188.4
44: (ns/day) (hour/ns)
44: Performance: 157.411 0.152
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 (612 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.614 0.307 199.7
44: (ns/day) (hour/ns)
44: Performance: 4.779 5.022
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.018 0.009 188.4
44: (ns/day) (hour/ns)
44: Performance: 155.949 0.154
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 (600 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.680 0.341 199.7
44: (ns/day) (hour/ns)
44: Performance: 4.312 5.566
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.018 0.009 188.5
44: (ns/day) (hour/ns)
44: Performance: 155.582 0.154
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 (633 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.658 0.330 199.7
44: (ns/day) (hour/ns)
44: Performance: 4.456 5.386
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.018 0.009 188.3
44: (ns/day) (hour/ns)
44: Performance: 156.890 0.153
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 (622 ms)
44: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.547 0.274 199.6
44: (ns/day) (hour/ns)
44: Performance: 5.356 4.481
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.trr'
44:
44:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.018 0.009 189.6
44: (ns/day) (hour/ns)
44: Performance: 156.994 0.153
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim2.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
44:
44: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 (567 ms)
44: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest (15746 ms total)
44:
44: [----------] 2 tests from Angles1/SimpleMdrunTest
44: [ RUN ] Angles1/SimpleMdrunTest.WithinTolerances/0
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44: Generated 3 of the 3 non-bonded parameter combinations
44: Excluding 3 bonded neighbours molecule type 'butane'
44:
44: NOTE 2 [file angles1.top, line 72]:
44: In moleculetype 'butane' 4 atoms are not bound by a potential or
44: constraint to any other atom in the same moleculetype. Although
44: technically this might not cause issues in a simulation, this often means
44: that the user forgot to add a bond/potential/constraint or put multiple
44: molecules in the same moleculetype definition by mistake. Run with -v to
44: get information for each atom.
44:
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_0_input.mdp]:
44: NVE simulation: will use the initial temperature of 238.919 K for
44: determining the Verlet buffer size
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'This_incredible_box_of_butane'
44: 50 steps, 0.1 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 238.919 K
44: Calculated rlist for 1x1 atom pair-list as 0.700 nm, buffer size 0.000 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.700 nm, buffer size 0.000 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.525 0.263 199.8
44: (ns/day) (hour/ns)
44: Performance: 16.780 1.430
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_0.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 5 time 0.020
Reading energy frame 6 time 0.024
Reading energy frame 7 time 0.028
Reading energy frame 8 time 0.032
Reading energy frame 9 time 0.036
Reading energy frame 10 time 0.040
Reading energy frame 11 time 0.044
Reading energy frame 12 time 0.048
Reading energy frame 13 time 0.050
Last energy frame read 13 time 0.050
44: [ OK ] Angles1/SimpleMdrunTest.WithinTolerances/0 (324 ms)
44: [ RUN ] Angles1/SimpleMdrunTest.WithinTolerances/1
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_1_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44: Generated 3 of the 3 non-bonded parameter combinations
44: Excluding 3 bonded neighbours molecule type 'butane'
44:
44: NOTE 2 [file angles1.top, line 72]:
44: In moleculetype 'butane' 4 atoms are not bound by a potential or
44: constraint to any other atom in the same moleculetype. Although
44: technically this might not cause issues in a simulation, this often means
44: that the user forgot to add a bond/potential/constraint or put multiple
44: molecules in the same moleculetype definition by mistake. Run with -v to
44: get information for each atom.
44:
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_1_input.mdp]:
44: NVE simulation: will use the initial temperature of 238.919 K for
44: determining the Verlet buffer size
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_1.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44: Using 2 OpenMP threads
44:
44:
44: NOTE: The number of threads is not equal to the number of (logical) cores
44: and the -pin option is set to auto: will not pin threads to cores.
44: This can lead to significant performance degradation.
44: Consider using -pin on (and -pinoffset in case you run multiple jobs).
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'This_incredible_box_of_butane'
44: 50 steps, 0.1 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 238.919 K
44: Calculated rlist for 1x1 atom pair-list as 0.700 nm, buffer size 0.000 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.700 nm, buffer size 0.000 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.388 0.194 199.8
44: (ns/day) (hour/ns)
44: Performance: 22.695 1.057
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_1.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 5 time 0.020
Reading energy frame 6 time 0.024
Reading energy frame 7 time 0.028
Reading energy frame 8 time 0.032
Reading energy frame 9 time 0.036
Reading energy frame 10 time 0.040
Reading energy frame 11 time 0.044
Reading energy frame 12 time 0.048
Reading energy frame 13 time 0.050
Last energy frame read 13 time 0.050
44: [ OK ] Angles1/SimpleMdrunTest.WithinTolerances/1 (242 ms)
44: [----------] 2 tests from Angles1/SimpleMdrunTest (568 ms total)
44:
44: [----------] Global test environment tear-down
44: [==========] 65 tests from 7 test cases ran. (80456 ms total)
44: [ PASSED ] 65 tests.
44/52 Test #44: MdrunNonIntegratorTests ............. Passed 80.65 sec
test 45
Start 45: MdrunTpiTests
45: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrun-tpi-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunTpiTests.xml"
45: Test timeout computed to be: 600
45: [==========] Running 2 tests from 1 test case.
45: [----------] Global test environment set-up.
45: [----------] 2 tests from Simple/TpiTest
45: [ RUN ] Simple/TpiTest.ReproducesOutput/0
45: Ignoring obsolete mdp entry 'ns_type'
45: Generated 331705 of the 331705 non-bonded parameter combinations
45: Generating 1-4 interactions: fudge = 0.5
45: Generated 331705 of the 331705 1-4 parameter combinations
45: Excluding 2 bonded neighbours molecule type 'SOL'
45: Excluding 3 bonded neighbours molecule type 'methane'
45: Number of degrees of freedom in T-Coupling group System is 1308.00
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
45: TPI is not implemented for GPUs.
45:
45: Using 1 MPI thread
45: Using 1 OpenMP thread
45:
45:
45: NOTE: Thread affinity was not set.
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: Reading frames from gro file '216 water molecules', 648 atoms.
45:
Reading frame 0 time 0.000 mu 8.706e+02 <mu> 8.706e+02
45:
Last frame 0 time 0.000
45: Analysing residue names:
45: There are: 216 Water residues
45: There are: 1 Other residues
45: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
45: This run will generate roughly 0 Mb of data
45: [ OK ] Simple/TpiTest.ReproducesOutput/0 (4644 ms)
45: [ RUN ] Simple/TpiTest.ReproducesOutput/1
45: Ignoring obsolete mdp entry 'ns_type'
45: Generated 331705 of the 331705 non-bonded parameter combinations
45: Generating 1-4 interactions: fudge = 0.5
45: Generated 331705 of the 331705 1-4 parameter combinations
45: Excluding 2 bonded neighbours molecule type 'SOL'
45: Excluding 3 bonded neighbours molecule type 'methane'
45: Number of degrees of freedom in T-Coupling group System is 1308.00
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_1.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
45: TPI is not implemented for GPUs.
45:
45: Using 1 MPI thread
45: Using 1 OpenMP thread
45:
45:
45: NOTE: Thread affinity was not set.
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: Reading frames from gro file '216 water molecules', 648 atoms.
45:
Reading frame 0 time 0.000 mu 9.144e+01 <mu> 9.144e+01
45:
Last frame 0 time 0.000
45: Analysing residue names:
45: There are: 216 Water residues
45: There are: 1 Other residues
45: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
45: This run will generate roughly 0 Mb of data
45: [ OK ] Simple/TpiTest.ReproducesOutput/1 (4665 ms)
45: [----------] 2 tests from Simple/TpiTest (9309 ms total)
45:
45: [----------] Global test environment tear-down
45: [==========] 2 tests from 1 test case ran. (9309 ms total)
45: [ PASSED ] 2 tests.
45/52 Test #45: MdrunTpiTests ....................... Passed 9.38 sec
test 46
Start 46: MdrunMpiTests
46: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrun-mpi-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunMpiTests.xml"
46: Test timeout computed to be: 600
46: [==========] Running 22 tests from 7 test cases.
46: [----------] Global test environment set-up.
46: [----------] 1 test from DomainDecompositionSpecialCasesTest
46: [ RUN ] DomainDecompositionSpecialCasesTest.AnEmptyDomainWorks
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]:
46: For a correct single-point energy evaluation with nsteps = 0, use
46: continuation = yes to avoid constraining the input coordinates.
46:
46: Setting the LD random seed to 2074257858
46: Generated 3 of the 3 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 3 of the 3 1-4 parameter combinations
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group rest is 9.00
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]:
46: NVE simulation with an initial temperature of zero: will use a Verlet
46: buffer of 10%. Check your energy drift!
46:
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 2 MPI threads
46: Using 2 OpenMP threads per tMPI thread
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'spc2'
46: 0 steps, 0.0 ps.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.006 0.002 322.3
46: (ns/day) (hour/ns)
46: Performance: 43.982 0.546
46: This run will generate roughly 0 Mb of data
46: [ OK ] DomainDecompositionSpecialCasesTest.AnEmptyDomainWorks (81 ms)
46: [----------] 1 test from DomainDecompositionSpecialCasesTest (81 ms total)
46:
46: [----------] 4 tests from MimicTest
46: [ RUN ] MimicTest.OneQuantumMol
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
46: For a correct single-point energy evaluation with nsteps = 0, use
46: continuation = yes to avoid constraining the input coordinates.
46:
46: Setting the LD random seed to 1500241079
46: Generated 10 of the 10 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 10 of the 10 1-4 parameter combinations
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group rest is 21.00
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
46: NVE simulation with an initial temperature of zero: will use a Verlet
46: buffer of 10%. Check your energy drift!
46:
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 2 MPI threads
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads per tMPI thread
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
46:
46: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
46:
Reading frame 0 time 0.000
Last frame 0 time 0.000
46:
46: Core t (s) Wall t (s) (%)
46: Time: 2.540 0.665 382.0
46: (ns/day) (hour/ns)
46: Performance: 0.130 184.714
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
46: [ OK ] MimicTest.OneQuantumMol (2089 ms)
46: [ RUN ] MimicTest.AllQuantumMol
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
46: For a correct single-point energy evaluation with nsteps = 0, use
46: continuation = yes to avoid constraining the input coordinates.
46:
46: Setting the LD random seed to 178944705
46: Generated 10 of the 10 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 10 of the 10 1-4 parameter combinations
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group rest is 21.00
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
46: NVE simulation with an initial temperature of zero: will use a Verlet
46: buffer of 10%. Check your energy drift!
46:
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 2 MPI threads
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads per tMPI thread
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
46:
46: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
46:
Reading frame 0 time 0.000
Last frame 0 time 0.000
46:
46: Core t (s) Wall t (s) (%)
46: Time: 2.560 0.670 382.1
46: (ns/day) (hour/ns)
46: Performance: 0.129 186.098
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
46: [ OK ] MimicTest.AllQuantumMol (2088 ms)
46: [ RUN ] MimicTest.TwoQuantumMol
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
46: For a correct single-point energy evaluation with nsteps = 0, use
46: continuation = yes to avoid constraining the input coordinates.
46:
46: Setting the LD random seed to 764298492
46: Generated 10 of the 10 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 10 of the 10 1-4 parameter combinations
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group rest is 21.00
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
46: NVE simulation with an initial temperature of zero: will use a Verlet
46: buffer of 10%. Check your energy drift!
46:
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 2 MPI threads
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads per tMPI thread
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
46:
46: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
46:
Reading frame 0 time 0.000
Last frame 0 time 0.000
46:
46: Core t (s) Wall t (s) (%)
46: Time: 2.520 0.660 381.9
46: (ns/day) (hour/ns)
46: Performance: 0.131 183.324
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
46: [ OK ] MimicTest.TwoQuantumMol (2050 ms)
46: [ RUN ] MimicTest.BondCuts
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
46: For a correct single-point energy evaluation with nsteps = 0, use
46: continuation = yes to avoid constraining the input coordinates.
46:
46: Setting the LD random seed to -2032842055
46: Generated 2211 of the 2211 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2211 of the 2211 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
46: Number of degrees of freedom in T-Coupling group rest is 66.00
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
46: NVE simulation: will use the initial temperature of 300.368 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 2 MPI threads
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads per tMPI thread
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/ala.gro'
46:
46: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms.
46:
Reading frame 0 time 0.000
Last frame 0 time 0.000
46:
46: Core t (s) Wall t (s) (%)
46: Time: 2.440 0.640 381.3
46: (ns/day) (hour/ns)
46: Performance: 0.135 177.757
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K
46: Calculated rlist for 1x1 atom pair-list as 1.034 nm, buffer size 0.034 nm
46: Set rlist, assuming 4x4 atom pair-list, to 1.025 nm, buffer size 0.025 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46: [ OK ] MimicTest.BondCuts (2102 ms)
46: [----------] 4 tests from MimicTest (8329 ms total)
46:
46: [----------] 1 test from MultiSimTerminationTest
46: [ RUN ] MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts
46: [ OK ] MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (1 ms)
46: [----------] 1 test from MultiSimTerminationTest (1 ms total)
46:
46: [----------] 3 tests from PmeTest
46: [ RUN ] PmeTest.ReproducesEnergies
46: Setting the LD random seed to 102405032
46: Generated 8 of the 10 non-bonded parameter combinations
46: Excluding 2 bonded neighbours molecule type 'Methanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group rest is 12.00
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
46: NVE simulation: will use the initial temperature of 1046.791 K for
46: determining the Verlet buffer size
46:
46: Estimate for the relative computational load of the PME mesh part: 1.00
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
46: The optimal PME mesh load for parallel simulations is below 0.5
46: and for highly parallel simulations between 0.25 and 0.33,
46: for higher performance, increase the cut-off and the PME grid spacing.
46:
46:
46:
46: There were 2 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 2 MPI threads
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads per tMPI thread
46: Using 0 OpenMP thread per tMPI thread for PME
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'spc-and-methanol'
46: 20 steps, 0.0 ps.
46: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
46: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
46: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: Calculating fourier grid dimensions for X Y Z
46: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 8.947 2.275 393.3
46: (ns/day) (hour/ns)
46: Performance: 0.798 30.090
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeAuto.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 2 MPI threads
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads per tMPI thread
46: Using 0 OpenMP thread per tMPI thread for PME
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'spc-and-methanol'
46: 20 steps, 0.0 ps.
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 8.939 2.275 393.0
46: (ns/day) (hour/ns)
46: Performance: 0.798 30.089
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpu.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 2 MPI threads
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads per tMPI thread
46: Using 0 OpenMP thread per tMPI thread for PME
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
46: starting mdrun 'spc-and-methanol'
46: 20 steps, 0.0 ps.
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 8.981 2.285 393.1
46: (ns/day) (hour/ns)
46: Performance: 0.794 30.221
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpuTune.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 [ OK ] PmeTest.ReproducesEnergies (9724 ms)
46: [ RUN ] PmeTest.ScalesTheBox
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
46: For a correct single-point energy evaluation with nsteps = 0, use
46: continuation = yes to avoid constraining the input coordinates.
46:
46: Setting the LD random seed to -967481482
46: Generated 8 of the 10 non-bonded parameter combinations
46: Excluding 2 bonded neighbours molecule type 'Methanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group rest is 12.00
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
46: NVE simulation: will use the initial temperature of 1046.791 K for
46: determining the Verlet buffer size
46:
46: Estimate for the relative computational load of the PME mesh part: 1.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
46: The optimal PME mesh load for parallel simulations is below 0.5
46: and for highly parallel simulations between 0.25 and 0.33,
46: for higher performance, increase the cut-off and the PME grid spacing.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 2 MPI threads
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads per tMPI thread
46: Using 0 OpenMP thread per tMPI thread for PME
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'spc-and-methanol'
46: 0 steps, 0.0 ps.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.381 0.135 282.4
46: (ns/day) (hour/ns)
46: Performance: 0.641 37.436
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_spc-and-methanol_PmeOnCpu.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
46: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
46: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: Calculating fourier grid dimensions for X Y Z
46: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107
46: This run will generate roughly 0 Mb of data
46: [ OK ] PmeTest.ScalesTheBox (1075 ms)
46: [ RUN ] PmeTest.ScalesTheBoxWithWalls
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
46: For a correct single-point energy evaluation with nsteps = 0, use
46: continuation = yes to avoid constraining the input coordinates.
46:
46: Setting the LD random seed to -1183261156
46: Generated 8 of the 10 non-bonded parameter combinations
46: Excluding 2 bonded neighbours molecule type 'Methanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Searching the wall atom type(s)
46: Number of degrees of freedom in T-Coupling group rest is 13.00
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
46: NVE simulation: will use the initial temperature of 966.268 K for
46: determining the Verlet buffer size
46:
46: Estimate for the relative computational load of the PME mesh part: 1.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
46: The optimal PME mesh load for parallel simulations is below 0.5
46: and for highly parallel simulations between 0.25 and 0.33,
46: for higher performance, increase the cut-off and the PME grid spacing.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 2 MPI threads
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads per tMPI thread
46: Using 0 OpenMP thread per tMPI thread for PME
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'spc-and-methanol'
46: 0 steps, 0.0 ps.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.761 0.230 331.1
46: (ns/day) (hour/ns)
46: Performance: 0.376 63.830
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_spc-and-methanol_PmeOnCpu.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K
46: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
46: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: Calculating fourier grid dimensions for X Y Z
46: Using a fourier grid of 28x28x128, spacing 0.107 0.107 0.118
46: This run will generate roughly 0 Mb of data
46: [ OK ] PmeTest.ScalesTheBoxWithWalls (1369 ms)
46: [----------] 3 tests from PmeTest (12168 ms total)
46:
46: [----------] 1 test from ReplicaExchangeTerminationTest
46: [ RUN ] ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts
46: [ OK ] ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (1 ms)
46: [----------] 1 test from ReplicaExchangeTerminationTest (1 ms total)
46:
46: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest
46: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 330891 of the 330891 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 330891 of the 330891 1-4 parameter combinations
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 27.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
46: Using 2 MPI threads
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads per tMPI thread
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Steepest Descents:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Steepest Descents did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = -4.79910463671071e+01
46: Maximum force = 1.86297359432218e+02 on atom 13
46: Norm of force = 8.77219865482161e+01
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (7256 ms)
46: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 330891 of the 330891 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 330891 of the 330891 1-4 parameter combinations
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 27.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
46: Using 2 MPI threads
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads per tMPI thread
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Polak-Ribiere Conjugate Gradients:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46: F-max = 3.02331e+02 on atom 3
46: F-Norm = 1.18024e+02
46:
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = -5.58622538633290e+01
46: Maximum force = 4.27274822366538e+02 on atom 13
46: Norm of force = 1.84530029253833e+02
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (8792 ms)
46: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 20503 of the 20503 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 1
46: Generated 17396 of the 20503 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Glycine'
46: Number of degrees of freedom in T-Coupling group System is 22.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
46: Using 2 MPI threads
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads per tMPI thread
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Steepest Descents:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Steepest Descents did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = 3.19376899751521e+02
46: Maximum force = 9.99884921009767e+03 on atom 9
46: Norm of force = 4.61669565054298e+03
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 turning H bonds into constraints...
46: This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (4273 ms)
46: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 20503 of the 20503 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 1
46: Generated 17396 of the 20503 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Glycine'
46:
46: NOTE 3 [file glycine_vacuo.top, line 12]:
46: For accurate cg with LINCS constraints, lincs-order should be 8 or more.
46:
46: Number of degrees of freedom in T-Coupling group System is 22.00
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
46: Using 2 MPI threads
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads per tMPI thread
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Polak-Ribiere Conjugate Gradients:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46: F-max = 2.41575e+04 on atom 10
46: F-Norm = 1.18451e+04
46:
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = 1.51743018140926e+02
46: Maximum force = 7.42089573409112e+03 on atom 9
46: Norm of force = 3.56929298615739e+03
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 turning H bonds into constraints...
46: This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (5818 ms)
46: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 2145 of the 2145 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2145 of the 2145 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
46:
46: NOTE 3 [file unknown]:
46: You are using constraints on all bonds, whereas the forcefield has been
46: parametrized only with constraints involving hydrogen atoms. We suggest
46: using constraints = h-bonds instead, this will also improve performance.
46:
46: Cleaning up constraints and constant bonded interactions with virtual sites
46: Removed 18 Angles with virtual sites, 21 left
46: Removed 10 Proper Dih.s with virtual sites, 44 left
46: Converted 15 Constraints with virtual sites to connections, 7 left
46: Number of degrees of freedom in T-Coupling group System is 23.00
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
46: Using 2 MPI threads
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads per tMPI thread
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Steepest Descents:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Steepest Descents did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = -1.56984193848276e+02
46: Maximum force = 4.56923624626296e+02 on atom 17
46: Norm of force = 1.83258377168331e+02
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 3.000
Last energy frame read 2 time 3.000 turning all bonds into constraints...
46: This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (4904 ms)
46: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 2145 of the 2145 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2145 of the 2145 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
46:
46: NOTE 3 [file unknown]:
46: You are using constraints on all bonds, whereas the forcefield has been
46: parametrized only with constraints involving hydrogen atoms. We suggest
46: using constraints = h-bonds instead, this will also improve performance.
46:
46:
46: NOTE 4 [file unknown]:
46: For accurate cg with LINCS constraints, lincs-order should be 8 or more.
46:
46: Cleaning up constraints and constant bonded interactions with virtual sites
46: Removed 18 Angles with virtual sites, 21 left
46: Removed 10 Proper Dih.s with virtual sites, 44 left
46: Converted 15 Constraints with virtual sites to connections, 7 left
46: Number of degrees of freedom in T-Coupling group System is 23.00
46:
46: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 5 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
46: Using 2 MPI threads
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads per tMPI thread
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Polak-Ribiere Conjugate Gradients:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46: F-max = 1.06800e+03 on atom 28
46: F-Norm = 4.26922e+02
46:
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = -1.69410778678185e+02
46: Maximum force = 2.18225948474048e+02 on atom 17
46: Norm of force = 7.92068036537643e+01
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 turning all bonds into constraints...
46: This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (7096 ms)
46: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (38141 ms total)
46:
46: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest
46: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 1 of the 1 non-bonded parameter combinations
46: Excluding 1 bonded neighbours molecule type 'Argon'
46: Number of degrees of freedom in T-Coupling group System is 33.00
46:
46: There were 2 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
46: Using 2 MPI threads
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads per tMPI thread
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Steepest Descents:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46:
46: writing lowest energy coordinates.
46:
46: Steepest Descents converged to Fmax < 10 in 1 steps
46: Potential Energy = -9.74257075835450e-01
46: Maximum force = 4.01322929015108e+00 on atom 3
46: Norm of force = 1.63839399694368e+00
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (1650 ms)
46: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 1 of the 1 non-bonded parameter combinations
46: Excluding 1 bonded neighbours molecule type 'Argon'
46: Number of degrees of freedom in T-Coupling group System is 33.00
46:
46: There were 2 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
46: Using 2 MPI threads
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads per tMPI thread
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Polak-Ribiere Conjugate Gradients:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46: F-max = 4.01323e+00 on atom 3
46: F-Norm = 1.63839e+00
46:
46:
46: writing lowest energy coordinates.
46:
46: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps
46: Potential Energy = -9.90642313893957e-01
46: Maximum force = 2.57812909491105e+00 on atom 3
46: Norm of force = 1.05251679559258e+00
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Last energy frame read 1 time 0.000 This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (2149 ms)
46: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46:
46: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
46: For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
46:
46: Generated 1 of the 1 non-bonded parameter combinations
46: Excluding 1 bonded neighbours molecule type 'Argon'
46: Number of degrees of freedom in T-Coupling group System is 33.00
46:
46: There were 2 notes
46:
46: There was 1 warning
46: This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (24 ms)
46: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 20503 of the 20503 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 1
46: Generated 17396 of the 20503 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Glycine'
46: Number of degrees of freedom in T-Coupling group System is 27.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
46: Using 2 MPI threads
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads per tMPI thread
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Steepest Descents:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Steepest Descents did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = 3.19395484891518e+02
46: Maximum force = 9.97041707197910e+03 on atom 9
46: Norm of force = 4.62274878665467e+03
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (3979 ms)
46: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 20503 of the 20503 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 1
46: Generated 17396 of the 20503 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Glycine'
46: Number of degrees of freedom in T-Coupling group System is 27.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
46: Using 2 MPI threads
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads per tMPI thread
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Polak-Ribiere Conjugate Gradients:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46: F-max = 2.41672e+04 on atom 10
46: F-Norm = 1.19357e+04
46:
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = 1.56258793899479e+02
46: Maximum force = 7.50181017480397e+03 on atom 9
46: Norm of force = 3.61390332564874e+03
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (5609 ms)
46: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46:
46: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
46: For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
46:
46: Generated 20503 of the 20503 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 1
46: Generated 17396 of the 20503 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Glycine'
46: Number of degrees of freedom in T-Coupling group System is 27.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46:
46: There was 1 warning
46: This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (1065 ms)
46: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (14479 ms total)
46:
46: [----------] Global test environment tear-down
46: [==========] 22 tests from 7 test cases ran. (73202 ms total)
46: [ PASSED ] 22 tests.
46:
46: YOU HAVE 4 DISABLED TESTS
46:
46/52 Test #46: MdrunMpiTests ....................... Passed 73.30 sec
test 47
Start 47: MdrunMpiCoordinationTestsOneRank
47: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrun-mpi-coordination-test "-ntmpi" "1" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunMpiCoordinationTestsOneRank.xml"
47: Test timeout computed to be: 480
47: [==========] Running 27 tests from 3 test cases.
47: [----------] Global test environment set-up.
47: [----------] 1 test from BasicPropagators/PeriodicActionsTest
47: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.192 0.193 99.9
47: (ns/day) (hour/ns)
47: Performance: 7.625 3.148
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.168 0.169 99.5
47: (ns/day) (hour/ns)
47: Performance: 8.676 2.766
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.163 0.165 99.2
47: (ns/day) (hour/ns)
47: Performance: 8.924 2.689
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.163 0.164 99.5
47: (ns/day) (hour/ns)
47: Performance: 8.969 2.676
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.188 0.189 99.8
47: (ns/day) (hour/ns)
47: Performance: 7.791 3.081
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.189 0.189 99.8
47: (ns/day) (hour/ns)
47: Performance: 7.755 3.095
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
47: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (1316 ms)
47: [----------] 1 test from BasicPropagators/PeriodicActionsTest (1316 ms total)
47:
47: [----------] 18 tests from PropagatorsWithCoupling/PeriodicActionsTest
47: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.184 0.185 99.9
47: (ns/day) (hour/ns)
47: Performance: 7.955 3.017
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.180 0.180 99.8
47: (ns/day) (hour/ns)
47: Performance: 8.162 2.940
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.175 0.176 99.8
47: (ns/day) (hour/ns)
47: Performance: 8.359 2.871
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.176 0.176 99.8
47: (ns/day) (hour/ns)
47: Performance: 8.344 2.876
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.177 0.178 99.8
47: (ns/day) (hour/ns)
47: Performance: 8.265 2.904
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.181 0.182 99.5
47: (ns/day) (hour/ns)
47: Performance: 8.053 2.980
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
47: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (1292 ms)
47: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.187 0.187 99.9
47: (ns/day) (hour/ns)
47: Performance: 7.837 3.062
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.185 0.185 99.8
47: (ns/day) (hour/ns)
47: Performance: 7.946 3.021
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.179 0.180 99.8
47: (ns/day) (hour/ns)
47: Performance: 8.181 2.934
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.179 0.180 99.8
47: (ns/day) (hour/ns)
47: Performance: 8.165 2.939
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.170 0.171 99.8
47: (ns/day) (hour/ns)
47: Performance: 8.597 2.792
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.184 0.185 99.8
47: (ns/day) (hour/ns)
47: Performance: 7.944 3.021
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
47: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (1331 ms)
47: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.180 0.180 99.9
47: (ns/day) (hour/ns)
47: Performance: 8.154 2.943
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.176 0.177 99.5
47: (ns/day) (hour/ns)
47: Performance: 8.296 2.893
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.181 0.183 99.3
47: (ns/day) (hour/ns)
47: Performance: 8.042 2.984
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.214 0.215 99.4
47: (ns/day) (hour/ns)
47: Performance: 6.818 3.520
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.194 0.195 99.4
47: (ns/day) (hour/ns)
47: Performance: 7.524 3.190
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.183 0.184 99.3
47: (ns/day) (hour/ns)
47: Performance: 7.969 3.012
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
47: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (1368 ms)
47: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.179 0.179 99.9
47: (ns/day) (hour/ns)
47: Performance: 8.198 2.928
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.188 0.188 99.8
47: (ns/day) (hour/ns)
47: Performance: 7.810 3.073
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.194 0.194 99.8
47: (ns/day) (hour/ns)
47: Performance: 7.557 3.176
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.172 0.172 99.8
47: (ns/day) (hour/ns)
47: Performance: 8.531 2.813
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.174 0.174 99.7
47: (ns/day) (hour/ns)
47: Performance: 8.426 2.848
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.185 0.185 99.8
47: (ns/day) (hour/ns)
47: Performance: 7.920 3.030
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
47: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (1320 ms)
47: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.192 0.192 99.9
47: (ns/day) (hour/ns)
47: Performance: 7.656 3.135
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.177 0.177 99.8
47: (ns/day) (hour/ns)
47: Performance: 8.293 2.894
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.194 0.194 99.8
47: (ns/day) (hour/ns)
47: Performance: 7.567 3.172
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.172 0.172 99.8
47: (ns/day) (hour/ns)
47: Performance: 8.541 2.810
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.174 0.174 99.8
47: (ns/day) (hour/ns)
47: Performance: 8.429 2.847
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.207 0.207 99.8
47: (ns/day) (hour/ns)
47: Performance: 7.092 3.384
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
47: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (1344 ms)
47: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.203 0.203 99.8
47: (ns/day) (hour/ns)
47: Performance: 7.226 3.321
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.212 0.212 99.8
47: (ns/day) (hour/ns)
47: Performance: 6.915 3.471
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.187 0.187 99.8
47: (ns/day) (hour/ns)
47: Performance: 7.850 3.057
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.209 0.209 99.8
47: (ns/day) (hour/ns)
47: Performance: 7.018 3.420
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.177 0.177 99.8
47: (ns/day) (hour/ns)
47: Performance: 8.282 2.898
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.177 0.177 99.8
47: (ns/day) (hour/ns)
47: Performance: 8.276 2.900
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
47: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (1377 ms)
47: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.218 0.218 99.9
47: (ns/day) (hour/ns)
47: Performance: 6.725 3.569
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.405 0.406 99.9
47: (ns/day) (hour/ns)
47: Performance: 3.621 6.628
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.174 0.174 99.5
47: (ns/day) (hour/ns)
47: Performance: 8.421 2.850
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.175 0.175 99.8
47: (ns/day) (hour/ns)
47: Performance: 8.371 2.867
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.200 0.200 99.8
47: (ns/day) (hour/ns)
47: Performance: 7.342 3.269
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.166 0.167 99.7
47: (ns/day) (hour/ns)
47: Performance: 8.803 2.726
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
47: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (1555 ms)
47: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
47:
47:
47: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: Using Berendsen pressure coupling invalidates the true ensemble for the
47: thermostat
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 3 notes
47:
47: There was 1 warning
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.173 0.173 99.9
47: (ns/day) (hour/ns)
47: Performance: 8.498 2.824
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
47:
47:
47: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: Using Berendsen pressure coupling invalidates the true ensemble for the
47: thermostat
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 3 notes
47:
47: There was 1 warning
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.180 0.180 99.8
47: (ns/day) (hour/ns)
47: Performance: 8.158 2.942
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
47:
47:
47: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: Using Berendsen pressure coupling invalidates the true ensemble for the
47: thermostat
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 3 notes
47:
47: There was 1 warning
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.175 0.176 99.8
47: (ns/day) (hour/ns)
47: Performance: 8.354 2.873
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
47:
47:
47: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: Using Berendsen pressure coupling invalidates the true ensemble for the
47: thermostat
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 3 notes
47:
47: There was 1 warning
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.153 0.154 99.7
47: (ns/day) (hour/ns)
47: Performance: 9.554 2.512
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
47:
47:
47: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: Using Berendsen pressure coupling invalidates the true ensemble for the
47: thermostat
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 3 notes
47:
47: There was 1 warning
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.188 0.189 99.8
47: (ns/day) (hour/ns)
47: Performance: 7.787 3.082
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
47:
47:
47: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: Using Berendsen pressure coupling invalidates the true ensemble for the
47: thermostat
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 3 notes
47:
47: There was 1 warning
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.221 0.222 99.8
47: (ns/day) (hour/ns)
47: Performance: 6.623 3.624
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
47: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (1300 ms)
47: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
47: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.217 0.218 99.9
47: (ns/day) (hour/ns)
47: Performance: 6.748 3.557
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
47: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.180 0.180 99.8
47: (ns/day) (hour/ns)
47: Performance: 8.165 2.939
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
47: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.176 0.176 99.8
47: (ns/day) (hour/ns)
47: Performance: 8.345 2.876
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
47: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.186 0.187 99.7
47: (ns/day) (hour/ns)
47: Performance: 7.858 3.054
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
47: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.200 0.200 99.8
47: (ns/day) (hour/ns)
47: Performance: 7.347 3.267
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
47: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.232 0.233 99.8
47: (ns/day) (hour/ns)
47: Performance: 6.305 3.806
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file
47: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (1400 ms)
47: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.162 0.162 99.9
47: (ns/day) (hour/ns)
47: Performance: 9.064 2.648
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.257 0.258 99.9
47: (ns/day) (hour/ns)
47: Performance: 5.697 4.213
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.176 0.176 99.7
47: (ns/day) (hour/ns)
47: Performance: 8.328 2.882
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.242 0.243 99.8
47: (ns/day) (hour/ns)
47: Performance: 6.052 3.966
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.177 0.178 99.8
47: (ns/day) (hour/ns)
47: Performance: 8.266 2.903
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.244 0.245 99.8
47: (ns/day) (hour/ns)
47: Performance: 6.006 3.996
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file
47: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (1467 ms)
47: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.184 0.184 99.9
47: (ns/day) (hour/ns)
47: Performance: 7.976 3.009
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.257 0.258 99.9
47: (ns/day) (hour/ns)
47: Performance: 5.700 4.211
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.175 0.176 99.8
47: (ns/day) (hour/ns)
47: Performance: 8.360 2.871
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.264 0.264 99.8
47: (ns/day) (hour/ns)
47: Performance: 5.553 4.322
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.264 0.264 99.8
47: (ns/day) (hour/ns)
47: Performance: 5.564 4.313
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.212 0.213 99.8
47: (ns/day) (hour/ns)
47: Performance: 6.905 3.476
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file
47: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (1567 ms)
47: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.284 0.284 99.9
47: (ns/day) (hour/ns)
47: Performance: 5.167 4.645
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.246 0.246 99.9
47: (ns/day) (hour/ns)
47: Performance: 5.961 4.026
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.275 0.276 99.9
47: (ns/day) (hour/ns)
47: Performance: 5.331 4.502
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.286 0.287 99.9
47: (ns/day) (hour/ns)
47: Performance: 5.121 4.687
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.210 0.211 99.8
47: (ns/day) (hour/ns)
47: Performance: 6.973 3.442
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.288 0.288 99.9
47: (ns/day) (hour/ns)
47: Performance: 5.092 4.713
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file
47: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (1800 ms)
47: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.174 0.174 99.9
47: (ns/day) (hour/ns)
47: Performance: 8.447 2.841
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.291 0.292 99.9
47: (ns/day) (hour/ns)
47: Performance: 5.036 4.765
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.173 0.173 99.9
47: (ns/day) (hour/ns)
47: Performance: 8.472 2.833
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.216 0.217 99.9
47: (ns/day) (hour/ns)
47: Performance: 6.783 3.538
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.163 0.163 99.9
47: (ns/day) (hour/ns)
47: Performance: 9.009 2.664
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.274 0.274 99.9
47: (ns/day) (hour/ns)
47: Performance: 5.356 4.481
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file
47: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (1512 ms)
47: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.269 0.269 99.9
47: (ns/day) (hour/ns)
47: Performance: 5.458 4.397
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.177 0.177 99.8
47: (ns/day) (hour/ns)
47: Performance: 8.305 2.890
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.260 0.261 99.8
47: (ns/day) (hour/ns)
47: Performance: 5.632 4.261
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.160 0.160 99.7
47: (ns/day) (hour/ns)
47: Performance: 9.161 2.620
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.274 0.274 99.9
47: (ns/day) (hour/ns)
47: Performance: 5.358 4.479
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
47: NVE simulation: will use the initial temperature of 68.810 K for
47: determining the Verlet buffer size
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.174 0.174 99.8
47: (ns/day) (hour/ns)
47: Performance: 8.445 2.842
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file
47: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (1544 ms)
47: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.281 0.281 99.9
47: (ns/day) (hour/ns)
47: Performance: 5.220 4.597
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.188 0.189 99.9
47: (ns/day) (hour/ns)
47: Performance: 7.788 3.082
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.189 0.189 99.9
47: (ns/day) (hour/ns)
47: Performance: 7.754 3.095
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.172 0.172 99.9
47: (ns/day) (hour/ns)
47: Performance: 8.525 2.815
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.219 0.219 99.9
47: (ns/day) (hour/ns)
47: Performance: 6.703 3.580
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.207 0.208 99.9
47: (ns/day) (hour/ns)
47: Performance: 7.073 3.393
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file
47: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (1489 ms)
47: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.202 0.202 99.9
47: (ns/day) (hour/ns)
47: Performance: 7.255 3.308
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.276 0.277 99.9
47: (ns/day) (hour/ns)
47: Performance: 5.306 4.523
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.171 0.172 99.7
47: (ns/day) (hour/ns)
47: Performance: 8.547 2.808
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.249 0.249 99.8
47: (ns/day) (hour/ns)
47: Performance: 5.894 4.072
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.177 0.177 99.8
47: (ns/day) (hour/ns)
47: Performance: 8.293 2.894
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.255 0.255 99.8
47: (ns/day) (hour/ns)
47: Performance: 5.755 4.171
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file
47: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (1554 ms)
47: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.162 0.162 99.9
47: (ns/day) (hour/ns)
47: Performance: 9.048 2.653
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.258 0.258 99.9
47: (ns/day) (hour/ns)
47: Performance: 5.692 4.217
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.143 0.143 99.7
47: (ns/day) (hour/ns)
47: Performance: 10.262 2.339
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.243 0.243 99.8
47: (ns/day) (hour/ns)
47: Performance: 6.047 3.969
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.144 0.144 99.7
47: (ns/day) (hour/ns)
47: Performance: 10.176 2.359
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.244 0.244 99.8
47: (ns/day) (hour/ns)
47: Performance: 6.010 3.993
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file
47: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (1400 ms)
47: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.184 0.185 99.8
47: (ns/day) (hour/ns)
47: Performance: 7.953 3.018
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.257 0.258 99.8
47: (ns/day) (hour/ns)
47: Performance: 5.695 4.214
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.208 0.209 99.8
47: (ns/day) (hour/ns)
47: Performance: 7.039 3.410
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.182 0.183 99.3
47: (ns/day) (hour/ns)
47: Performance: 8.012 2.996
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.186 0.187 99.3
47: (ns/day) (hour/ns)
47: Performance: 7.847 3.058
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 1 of the 1 non-bonded parameter combinations
47: Excluding 1 bonded neighbours molecule type 'Argon'
47: Number of degrees of freedom in T-Coupling group System is 33.00
47:
47: There were 2 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'Argon'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
47: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.230 0.232 99.5
47: (ns/day) (hour/ns)
47: Performance: 6.343 3.784
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file
47: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (1469 ms)
47: [----------] 18 tests from PropagatorsWithCoupling/PeriodicActionsTest (26092 ms total)
47:
47: [----------] 8 tests from PropagatorsWithConstraints/PeriodicActionsTest
47: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: NVE simulation: will use the initial temperature of 398.997 K for
47: determining the Verlet buffer size
47:
47:
47: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 4 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
47: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.306 0.307 99.9
47: (ns/day) (hour/ns)
47: Performance: 4.791 5.010
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: NVE simulation: will use the initial temperature of 398.997 K for
47: determining the Verlet buffer size
47:
47:
47: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 4 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
47: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.251 0.251 99.8
47: (ns/day) (hour/ns)
47: Performance: 5.846 4.105
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: NVE simulation: will use the initial temperature of 398.997 K for
47: determining the Verlet buffer size
47:
47:
47: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 4 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
47: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.274 0.274 99.8
47: (ns/day) (hour/ns)
47: Performance: 5.358 4.480
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: NVE simulation: will use the initial temperature of 398.997 K for
47: determining the Verlet buffer size
47:
47:
47: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 4 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
47: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.258 0.258 99.8
47: (ns/day) (hour/ns)
47: Performance: 5.692 4.217
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: NVE simulation: will use the initial temperature of 398.997 K for
47: determining the Verlet buffer size
47:
47:
47: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 4 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
47: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.254 0.255 99.8
47: (ns/day) (hour/ns)
47: Performance: 5.771 4.159
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: NVE simulation: will use the initial temperature of 398.997 K for
47: determining the Verlet buffer size
47:
47:
47: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 4 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
47: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.267 0.267 99.8
47: (ns/day) (hour/ns)
47: Performance: 5.491 4.371
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
47: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (26622 ms)
47: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: NVE simulation: will use the initial temperature of 398.997 K for
47: determining the Verlet buffer size
47:
47:
47: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 4 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
47: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.285 0.285 99.9
47: (ns/day) (hour/ns)
47: Performance: 5.148 4.662
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: NVE simulation: will use the initial temperature of 398.997 K for
47: determining the Verlet buffer size
47:
47:
47: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 4 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
47: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.257 0.257 99.8
47: (ns/day) (hour/ns)
47: Performance: 5.706 4.206
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: NVE simulation: will use the initial temperature of 398.997 K for
47: determining the Verlet buffer size
47:
47:
47: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 4 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
47: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.264 0.265 99.8
47: (ns/day) (hour/ns)
47: Performance: 5.551 4.323
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: NVE simulation: will use the initial temperature of 398.997 K for
47: determining the Verlet buffer size
47:
47:
47: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 4 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
47: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.309 0.309 99.8
47: (ns/day) (hour/ns)
47: Performance: 4.748 5.055
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: NVE simulation: will use the initial temperature of 398.997 K for
47: determining the Verlet buffer size
47:
47:
47: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 4 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
47: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.284 0.284 99.8
47: (ns/day) (hour/ns)
47: Performance: 5.163 4.648
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: NVE simulation: will use the initial temperature of 398.997 K for
47: determining the Verlet buffer size
47:
47:
47: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 4 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
47: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.287 0.287 99.8
47: (ns/day) (hour/ns)
47: Performance: 5.117 4.691
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
47: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (26535 ms)
47: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.289 0.290 99.9
47: (ns/day) (hour/ns)
47: Performance: 5.073 4.731
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.218 0.218 99.8
47: (ns/day) (hour/ns)
47: Performance: 6.726 3.568
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.274 0.275 99.8
47: (ns/day) (hour/ns)
47: Performance: 5.347 4.489
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.263 0.264 99.5
47: (ns/day) (hour/ns)
47: Performance: 5.558 4.318
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.256 0.257 99.8
47: (ns/day) (hour/ns)
47: Performance: 5.725 4.192
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.253 0.253 99.8
47: (ns/day) (hour/ns)
47: Performance: 5.802 4.136
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
47: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (26400 ms)
47: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.285 0.285 99.9
47: (ns/day) (hour/ns)
47: Performance: 5.147 4.663
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.269 0.270 99.9
47: (ns/day) (hour/ns)
47: Performance: 5.444 4.408
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.302 0.302 99.8
47: (ns/day) (hour/ns)
47: Performance: 4.861 4.937
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.281 0.282 99.8
47: (ns/day) (hour/ns)
47: Performance: 5.213 4.604
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.229 0.229 99.8
47: (ns/day) (hour/ns)
47: Performance: 6.406 3.747
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.291 0.291 99.8
47: (ns/day) (hour/ns)
47: Performance: 5.045 4.757
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
47: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (26546 ms)
47: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.267 0.267 99.9
47: (ns/day) (hour/ns)
47: Performance: 5.493 4.369
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.261 0.262 99.9
47: (ns/day) (hour/ns)
47: Performance: 5.613 4.276
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.270 0.271 99.8
47: (ns/day) (hour/ns)
47: Performance: 5.426 4.423
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.257 0.258 99.8
47: (ns/day) (hour/ns)
47: Performance: 5.697 4.213
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.256 0.256 99.8
47: (ns/day) (hour/ns)
47: Performance: 5.727 4.191
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.258 0.259 99.8
47: (ns/day) (hour/ns)
47: Performance: 5.680 4.226
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
47: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (26444 ms)
47: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.248 0.248 99.9
47: (ns/day) (hour/ns)
47: Performance: 5.926 4.050
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.252 0.252 99.8
47: (ns/day) (hour/ns)
47: Performance: 5.818 4.125
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.192 0.192 99.8
47: (ns/day) (hour/ns)
47: Performance: 7.630 3.145
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.205 0.205 99.8
47: (ns/day) (hour/ns)
47: Performance: 7.166 3.349
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.187 0.187 99.8
47: (ns/day) (hour/ns)
47: Performance: 7.843 3.060
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.183 0.183 99.8
47: (ns/day) (hour/ns)
47: Performance: 8.024 2.991
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
47: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (26268 ms)
47: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: NVE simulation: will use the initial temperature of 398.997 K for
47: determining the Verlet buffer size
47:
47:
47: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 4 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
47: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.198 0.198 99.9
47: (ns/day) (hour/ns)
47: Performance: 7.427 3.231
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: NVE simulation: will use the initial temperature of 398.997 K for
47: determining the Verlet buffer size
47:
47:
47: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 4 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
47: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.171 0.171 99.9
47: (ns/day) (hour/ns)
47: Performance: 8.581 2.797
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: NVE simulation: will use the initial temperature of 398.997 K for
47: determining the Verlet buffer size
47:
47:
47: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 4 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
47: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.161 0.162 99.9
47: (ns/day) (hour/ns)
47: Performance: 9.095 2.639
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: NVE simulation: will use the initial temperature of 398.997 K for
47: determining the Verlet buffer size
47:
47:
47: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 4 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
47: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.164 0.165 99.9
47: (ns/day) (hour/ns)
47: Performance: 8.922 2.690
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: NVE simulation: will use the initial temperature of 398.997 K for
47: determining the Verlet buffer size
47:
47:
47: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 4 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
47: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.176 0.177 99.9
47: (ns/day) (hour/ns)
47: Performance: 8.317 2.886
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: NVE simulation: will use the initial temperature of 398.997 K for
47: determining the Verlet buffer size
47:
47:
47: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 4 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Can not increase nstlist because an NVE ensemble is used
47: Using 1 MPI thread
47: Using 1 OpenMP thread
47:
47:
47: NOTE: Thread affinity was not set.
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
47: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.167 0.167 99.9
47: (ns/day) (hour/ns)
47: Performance: 8.811 2.724
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
47: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (25904 ms)
47: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47: Using 1 OpenMP thread
47:
47:
47: NOTE: Thread affinity was not set.
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.180 0.180 99.9
47: (ns/day) (hour/ns)
47: Performance: 8.140 2.948
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.172 0.172 99.9
47: (ns/day) (hour/ns)
47: Performance: 8.516 2.818
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.215 0.215 99.9
47: (ns/day) (hour/ns)
47: Performance: 6.819 3.520
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
47:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.180 0.180 99.9
47: (ns/day) (hour/ns)
47: Performance: 8.162 2.941
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.175 0.175 99.9
47: (ns/day) (hour/ns)
47: Performance: 8.371 2.867
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
47:
47: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
47: that with the Verlet scheme, nstlist has no effect on the accuracy of
47: your simulation.
47:
47:
47: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: Setting nstcalcenergy (100) equal to nstenergy (4)
47:
47: Generated 330891 of the 330891 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 330891 of the 330891 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Number of degrees of freedom in T-Coupling group System is 27.00
47:
47: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
47: You are using a plain Coulomb cut-off, which might produce artifacts.
47: You might want to consider using PME electrostatics.
47:
47:
47:
47: There were 3 notes
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
47: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: starting mdrun 'spc2'
47: 16 steps, 0.0 ps.
47: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
47: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
47: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
47: Note that mdrun will redetermine rlist based on the actual pair-list setup
47: This run will generate roughly 0 Mb of data
47:
47: Writing final coordinates.
47:
47: Core t (s) Wall t (s) (%)
47: Time: 0.177 0.177 99.9
47: (ns/day) (hour/ns)
47: Performance: 8.297 2.893
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
47: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
47: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (25953 ms)
47: [----------] 8 tests from PropagatorsWithConstraints/PeriodicActionsTest (210673 ms total)
47:
47: [----------] Global test environment tear-down
47: [==========] 27 tests from 3 test cases ran. (238081 ms total)
47: [ PASSED ] 27 tests.
47/52 Test #47: MdrunMpiCoordinationTestsOneRank .... Passed 238.17 sec
test 48
Start 48: MdrunMpiCoordinationTestsTwoRanks
48: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrun-mpi-coordination-test "-ntmpi" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunMpiCoordinationTestsTwoRanks.xml"
48: Test timeout computed to be: 480
48: [==========] Running 27 tests from 3 test cases.
48: [----------] Global test environment set-up.
48: [----------] 1 test from BasicPropagators/PeriodicActionsTest
48: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.379 0.190 199.7
48: (ns/day) (hour/ns)
48: Performance: 7.735 3.103
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.332 0.167 199.3
48: (ns/day) (hour/ns)
48: Performance: 8.810 2.724
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.349 0.175 199.4
48: (ns/day) (hour/ns)
48: Performance: 8.402 2.856
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.416 0.208 199.4
48: (ns/day) (hour/ns)
48: Performance: 7.047 3.406
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.351 0.176 199.3
48: (ns/day) (hour/ns)
48: Performance: 8.342 2.877
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.529 0.265 199.6
48: (ns/day) (hour/ns)
48: Performance: 5.543 4.330
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
48: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (1435 ms)
48: [----------] 1 test from BasicPropagators/PeriodicActionsTest (1435 ms total)
48:
48: [----------] 18 tests from PropagatorsWithCoupling/PeriodicActionsTest
48: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.370 0.185 199.7
48: (ns/day) (hour/ns)
48: Performance: 7.932 3.026
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.509 0.255 199.6
48: (ns/day) (hour/ns)
48: Performance: 5.753 4.172
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.347 0.174 199.4
48: (ns/day) (hour/ns)
48: Performance: 8.441 2.843
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.482 0.241 199.5
48: (ns/day) (hour/ns)
48: Performance: 6.084 3.945
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.522 0.262 199.5
48: (ns/day) (hour/ns)
48: Performance: 5.611 4.277
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.376 0.189 199.5
48: (ns/day) (hour/ns)
48: Performance: 7.787 3.082
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
48: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (1522 ms)
48: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.569 0.285 199.8
48: (ns/day) (hour/ns)
48: Performance: 5.158 4.653
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.398 0.199 199.5
48: (ns/day) (hour/ns)
48: Performance: 7.368 3.257
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.547 0.274 199.6
48: (ns/day) (hour/ns)
48: Performance: 5.361 4.476
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.369 0.185 199.4
48: (ns/day) (hour/ns)
48: Performance: 7.943 3.021
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.527 0.264 199.6
48: (ns/day) (hour/ns)
48: Performance: 5.557 4.319
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.545 0.273 199.6
48: (ns/day) (hour/ns)
48: Performance: 5.381 4.460
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
48: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (1698 ms)
48: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.351 0.176 199.6
48: (ns/day) (hour/ns)
48: Performance: 8.354 2.873
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.529 0.265 199.7
48: (ns/day) (hour/ns)
48: Performance: 5.543 4.330
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.347 0.174 199.4
48: (ns/day) (hour/ns)
48: Performance: 8.445 2.842
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.524 0.263 199.6
48: (ns/day) (hour/ns)
48: Performance: 5.592 4.292
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.349 0.175 199.4
48: (ns/day) (hour/ns)
48: Performance: 8.384 2.863
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.528 0.264 199.5
48: (ns/day) (hour/ns)
48: Performance: 5.556 4.320
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
48: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (1535 ms)
48: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.322 0.162 199.6
48: (ns/day) (hour/ns)
48: Performance: 9.090 2.640
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.531 0.266 199.6
48: (ns/day) (hour/ns)
48: Performance: 5.525 4.344
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.301 0.151 199.1
48: (ns/day) (hour/ns)
48: Performance: 9.703 2.473
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.545 0.273 199.6
48: (ns/day) (hour/ns)
48: Performance: 5.383 4.459
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.409 0.205 199.4
48: (ns/day) (hour/ns)
48: Performance: 7.164 3.350
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.482 0.242 199.5
48: (ns/day) (hour/ns)
48: Performance: 6.074 3.951
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
48: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (1523 ms)
48: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.567 0.284 199.7
48: (ns/day) (hour/ns)
48: Performance: 5.176 4.637
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.419 0.210 199.5
48: (ns/day) (hour/ns)
48: Performance: 6.997 3.430
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.545 0.273 199.6
48: (ns/day) (hour/ns)
48: Performance: 5.378 4.463
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.412 0.206 199.5
48: (ns/day) (hour/ns)
48: Performance: 7.114 3.374
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.482 0.241 199.5
48: (ns/day) (hour/ns)
48: Performance: 6.082 3.946
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.482 0.242 199.6
48: (ns/day) (hour/ns)
48: Performance: 6.077 3.949
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
48: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (1677 ms)
48: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.367 0.184 199.6
48: (ns/day) (hour/ns)
48: Performance: 7.987 3.005
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.508 0.254 199.6
48: (ns/day) (hour/ns)
48: Performance: 5.775 4.156
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.367 0.184 199.4
48: (ns/day) (hour/ns)
48: Performance: 7.986 3.005
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.545 0.273 199.6
48: (ns/day) (hour/ns)
48: Performance: 5.380 4.461
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.348 0.175 199.4
48: (ns/day) (hour/ns)
48: Performance: 8.409 2.854
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.570 0.286 199.6
48: (ns/day) (hour/ns)
48: Performance: 5.141 4.668
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
48: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (1578 ms)
48: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.323 0.162 199.6
48: (ns/day) (hour/ns)
48: Performance: 9.080 2.643
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.486 0.243 199.6
48: (ns/day) (hour/ns)
48: Performance: 6.037 3.975
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.302 0.151 199.3
48: (ns/day) (hour/ns)
48: Performance: 9.697 2.475
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.546 0.273 199.6
48: (ns/day) (hour/ns)
48: Performance: 5.373 4.467
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.549 0.275 199.5
48: (ns/day) (hour/ns)
48: Performance: 5.335 4.499
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.349 0.176 198.8
48: (ns/day) (hour/ns)
48: Performance: 8.366 2.869
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
48: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (1501 ms)
48: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
48:
48:
48: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: Using Berendsen pressure coupling invalidates the true ensemble for the
48: thermostat
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 3 notes
48:
48: There was 1 warning
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.545 0.273 199.7
48: (ns/day) (hour/ns)
48: Performance: 5.383 4.459
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
48:
48:
48: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: Using Berendsen pressure coupling invalidates the true ensemble for the
48: thermostat
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 3 notes
48:
48: There was 1 warning
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.439 0.221 199.1
48: (ns/day) (hour/ns)
48: Performance: 6.660 3.603
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
48:
48:
48: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: Using Berendsen pressure coupling invalidates the true ensemble for the
48: thermostat
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 3 notes
48:
48: There was 1 warning
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.431 0.217 198.7
48: (ns/day) (hour/ns)
48: Performance: 6.779 3.541
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
48:
48:
48: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: Using Berendsen pressure coupling invalidates the true ensemble for the
48: thermostat
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 3 notes
48:
48: There was 1 warning
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.363 0.183 198.5
48: (ns/day) (hour/ns)
48: Performance: 8.029 2.989
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
48:
48:
48: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: Using Berendsen pressure coupling invalidates the true ensemble for the
48: thermostat
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 3 notes
48:
48: There was 1 warning
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.500 0.251 198.9
48: (ns/day) (hour/ns)
48: Performance: 5.843 4.107
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
48:
48:
48: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: Using Berendsen pressure coupling invalidates the true ensemble for the
48: thermostat
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 3 notes
48:
48: There was 1 warning
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.344 0.173 198.5
48: (ns/day) (hour/ns)
48: Performance: 8.466 2.835
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
48: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (1546 ms)
48: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
48: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.476 0.238 199.7
48: (ns/day) (hour/ns)
48: Performance: 6.163 3.894
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
48: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.573 0.287 199.3
48: (ns/day) (hour/ns)
48: Performance: 5.114 4.693
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
48: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.341 0.172 198.4
48: (ns/day) (hour/ns)
48: Performance: 8.536 2.812
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
48: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.534 0.268 199.0
48: (ns/day) (hour/ns)
48: Performance: 5.475 4.384
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
48: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.395 0.199 198.6
48: (ns/day) (hour/ns)
48: Performance: 7.377 3.253
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
48: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.593 0.298 199.1
48: (ns/day) (hour/ns)
48: Performance: 4.932 4.867
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file
48: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (1717 ms)
48: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.528 0.264 199.7
48: (ns/day) (hour/ns)
48: Performance: 5.558 4.318
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.320 0.161 198.8
48: (ns/day) (hour/ns)
48: Performance: 9.129 2.629
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.529 0.265 199.6
48: (ns/day) (hour/ns)
48: Performance: 5.537 4.334
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.367 0.184 199.4
48: (ns/day) (hour/ns)
48: Performance: 7.977 3.009
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.526 0.264 199.5
48: (ns/day) (hour/ns)
48: Performance: 5.574 4.306
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 1.147 0.574 199.8
48: (ns/day) (hour/ns)
48: Performance: 2.560 9.377
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file
48: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (2005 ms)
48: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.555 0.278 199.7
48: (ns/day) (hour/ns)
48: Performance: 5.283 4.542
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.407 0.204 199.5
48: (ns/day) (hour/ns)
48: Performance: 7.203 3.332
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.515 0.258 199.5
48: (ns/day) (hour/ns)
48: Performance: 5.688 4.219
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.531 0.266 199.6
48: (ns/day) (hour/ns)
48: Performance: 5.520 4.347
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.363 0.182 199.4
48: (ns/day) (hour/ns)
48: Performance: 8.069 2.974
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.519 0.260 199.6
48: (ns/day) (hour/ns)
48: Performance: 5.648 4.250
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file
48: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (1698 ms)
48: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.359 0.180 199.6
48: (ns/day) (hour/ns)
48: Performance: 8.175 2.936
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.523 0.262 199.6
48: (ns/day) (hour/ns)
48: Performance: 5.602 4.285
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.333 0.167 199.3
48: (ns/day) (hour/ns)
48: Performance: 8.796 2.729
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.490 0.246 199.4
48: (ns/day) (hour/ns)
48: Performance: 5.973 4.018
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.363 0.182 199.2
48: (ns/day) (hour/ns)
48: Performance: 8.059 2.978
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.447 0.224 199.4
48: (ns/day) (hour/ns)
48: Performance: 6.547 3.666
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file
48: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (1511 ms)
48: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.559 0.280 199.4
48: (ns/day) (hour/ns)
48: Performance: 5.242 4.579
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.364 0.183 199.0
48: (ns/day) (hour/ns)
48: Performance: 8.027 2.990
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.447 0.225 199.1
48: (ns/day) (hour/ns)
48: Performance: 6.539 3.670
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.381 0.192 198.7
48: (ns/day) (hour/ns)
48: Performance: 7.653 3.136
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.541 0.272 199.3
48: (ns/day) (hour/ns)
48: Performance: 5.407 4.439
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.383 0.192 199.0
48: (ns/day) (hour/ns)
48: Performance: 7.636 3.143
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file
48: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (1589 ms)
48: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.512 0.257 199.7
48: (ns/day) (hour/ns)
48: Performance: 5.725 4.192
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.567 0.284 199.7
48: (ns/day) (hour/ns)
48: Performance: 5.169 4.643
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.359 0.181 199.0
48: (ns/day) (hour/ns)
48: Performance: 8.134 2.951
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.536 0.268 199.6
48: (ns/day) (hour/ns)
48: Performance: 5.474 4.384
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.360 0.180 199.4
48: (ns/day) (hour/ns)
48: Performance: 8.138 2.949
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
48: NVE simulation: will use the initial temperature of 68.810 K for
48: determining the Verlet buffer size
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.514 0.258 199.6
48: (ns/day) (hour/ns)
48: Performance: 5.703 4.209
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file
48: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (1677 ms)
48: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.359 0.180 199.1
48: (ns/day) (hour/ns)
48: Performance: 8.147 2.946
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.568 0.285 199.4
48: (ns/day) (hour/ns)
48: Performance: 5.157 4.654
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.515 0.258 199.3
48: (ns/day) (hour/ns)
48: Performance: 5.689 4.219
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.337 0.170 198.6
48: (ns/day) (hour/ns)
48: Performance: 8.651 2.774
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.474 0.238 199.2
48: (ns/day) (hour/ns)
48: Performance: 6.170 3.890
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.365 0.183 198.7
48: (ns/day) (hour/ns)
48: Performance: 8.005 2.998
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file
48: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (1555 ms)
48: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.579 0.290 199.7
48: (ns/day) (hour/ns)
48: Performance: 5.066 4.737
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.434 0.217 199.5
48: (ns/day) (hour/ns)
48: Performance: 6.754 3.553
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.536 0.269 199.6
48: (ns/day) (hour/ns)
48: Performance: 5.468 4.389
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.536 0.269 199.6
48: (ns/day) (hour/ns)
48: Performance: 5.470 4.387
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.363 0.182 199.1
48: (ns/day) (hour/ns)
48: Performance: 8.056 2.979
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.496 0.249 199.5
48: (ns/day) (hour/ns)
48: Performance: 5.910 4.061
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file
48: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (1721 ms)
48: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.382 0.191 199.6
48: (ns/day) (hour/ns)
48: Performance: 7.679 3.125
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.501 0.251 199.6
48: (ns/day) (hour/ns)
48: Performance: 5.850 4.102
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.337 0.169 199.3
48: (ns/day) (hour/ns)
48: Performance: 8.688 2.762
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.359 0.180 199.3
48: (ns/day) (hour/ns)
48: Performance: 8.153 2.944
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.359 0.180 199.4
48: (ns/day) (hour/ns)
48: Performance: 8.157 2.942
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.450 0.226 199.5
48: (ns/day) (hour/ns)
48: Performance: 6.505 3.689
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file
48: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (1445 ms)
48: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.533 0.267 199.7
48: (ns/day) (hour/ns)
48: Performance: 5.508 4.357
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.371 0.186 199.5
48: (ns/day) (hour/ns)
48: Performance: 7.895 3.040
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.537 0.269 199.6
48: (ns/day) (hour/ns)
48: Performance: 5.461 4.395
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.403 0.202 199.4
48: (ns/day) (hour/ns)
48: Performance: 7.272 3.301
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.518 0.260 199.4
48: (ns/day) (hour/ns)
48: Performance: 5.650 4.248
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'Argon'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
48: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.363 0.182 198.9
48: (ns/day) (hour/ns)
48: Performance: 8.053 2.980
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file
48: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (1611 ms)
48: [----------] 18 tests from PropagatorsWithCoupling/PeriodicActionsTest (29115 ms total)
48:
48: [----------] 8 tests from PropagatorsWithConstraints/PeriodicActionsTest
48: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: NVE simulation: will use the initial temperature of 398.997 K for
48: determining the Verlet buffer size
48:
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
48: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.589 0.295 199.8
48: (ns/day) (hour/ns)
48: Performance: 4.978 4.821
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: NVE simulation: will use the initial temperature of 398.997 K for
48: determining the Verlet buffer size
48:
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
48: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.537 0.269 199.3
48: (ns/day) (hour/ns)
48: Performance: 5.454 4.400
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: NVE simulation: will use the initial temperature of 398.997 K for
48: determining the Verlet buffer size
48:
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
48: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.509 0.256 198.9
48: (ns/day) (hour/ns)
48: Performance: 5.735 4.185
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: NVE simulation: will use the initial temperature of 398.997 K for
48: determining the Verlet buffer size
48:
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
48: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.544 0.272 199.6
48: (ns/day) (hour/ns)
48: Performance: 5.392 4.451
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: NVE simulation: will use the initial temperature of 398.997 K for
48: determining the Verlet buffer size
48:
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
48: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.536 0.268 199.6
48: (ns/day) (hour/ns)
48: Performance: 5.472 4.386
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: NVE simulation: will use the initial temperature of 398.997 K for
48: determining the Verlet buffer size
48:
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
48: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.491 0.246 199.5
48: (ns/day) (hour/ns)
48: Performance: 5.966 4.023
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
48: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (27814 ms)
48: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: NVE simulation: will use the initial temperature of 398.997 K for
48: determining the Verlet buffer size
48:
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
48: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.522 0.261 199.7
48: (ns/day) (hour/ns)
48: Performance: 5.624 4.267
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: NVE simulation: will use the initial temperature of 398.997 K for
48: determining the Verlet buffer size
48:
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
48: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.563 0.282 199.6
48: (ns/day) (hour/ns)
48: Performance: 5.209 4.608
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: NVE simulation: will use the initial temperature of 398.997 K for
48: determining the Verlet buffer size
48:
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
48: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.512 0.256 199.5
48: (ns/day) (hour/ns)
48: Performance: 5.728 4.190
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: NVE simulation: will use the initial temperature of 398.997 K for
48: determining the Verlet buffer size
48:
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
48: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.500 0.251 198.9
48: (ns/day) (hour/ns)
48: Performance: 5.845 4.106
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: NVE simulation: will use the initial temperature of 398.997 K for
48: determining the Verlet buffer size
48:
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
48: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.539 0.271 199.0
48: (ns/day) (hour/ns)
48: Performance: 5.426 4.423
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: NVE simulation: will use the initial temperature of 398.997 K for
48: determining the Verlet buffer size
48:
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
48: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.508 0.256 198.8
48: (ns/day) (hour/ns)
48: Performance: 5.745 4.177
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
48: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (27089 ms)
48: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.578 0.289 199.7
48: (ns/day) (hour/ns)
48: Performance: 5.076 4.728
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.505 0.254 199.2
48: (ns/day) (hour/ns)
48: Performance: 5.790 4.145
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.493 0.248 198.7
48: (ns/day) (hour/ns)
48: Performance: 5.924 4.052
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.545 0.274 198.9
48: (ns/day) (hour/ns)
48: Performance: 5.358 4.479
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.525 0.263 199.5
48: (ns/day) (hour/ns)
48: Performance: 5.584 4.298
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.508 0.254 199.5
48: (ns/day) (hour/ns)
48: Performance: 5.771 4.158
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
48: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (26854 ms)
48: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.646 0.324 199.7
48: (ns/day) (hour/ns)
48: Performance: 4.539 5.288
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.506 0.254 199.6
48: (ns/day) (hour/ns)
48: Performance: 5.790 4.145
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.561 0.281 199.5
48: (ns/day) (hour/ns)
48: Performance: 5.226 4.593
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.489 0.245 199.5
48: (ns/day) (hour/ns)
48: Performance: 5.986 4.010
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.518 0.260 199.5
48: (ns/day) (hour/ns)
48: Performance: 5.652 4.246
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.541 0.271 199.5
48: (ns/day) (hour/ns)
48: Performance: 5.420 4.428
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
48: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (26957 ms)
48: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.548 0.274 199.7
48: (ns/day) (hour/ns)
48: Performance: 5.353 4.483
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.513 0.257 199.6
48: (ns/day) (hour/ns)
48: Performance: 5.710 4.203
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.515 0.258 199.5
48: (ns/day) (hour/ns)
48: Performance: 5.691 4.217
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.520 0.261 199.5
48: (ns/day) (hour/ns)
48: Performance: 5.632 4.262
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.525 0.263 199.5
48: (ns/day) (hour/ns)
48: Performance: 5.578 4.302
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.521 0.261 199.5
48: (ns/day) (hour/ns)
48: Performance: 5.629 4.263
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
48: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (26936 ms)
48: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.571 0.286 199.7
48: (ns/day) (hour/ns)
48: Performance: 5.140 4.669
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.552 0.276 199.6
48: (ns/day) (hour/ns)
48: Performance: 5.314 4.516
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.512 0.256 199.5
48: (ns/day) (hour/ns)
48: Performance: 5.729 4.189
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.516 0.259 199.5
48: (ns/day) (hour/ns)
48: Performance: 5.678 4.227
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.425 0.213 199.4
48: (ns/day) (hour/ns)
48: Performance: 6.884 3.486
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.354 0.178 199.3
48: (ns/day) (hour/ns)
48: Performance: 8.274 2.900
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
48: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (26811 ms)
48: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: NVE simulation: will use the initial temperature of 398.997 K for
48: determining the Verlet buffer size
48:
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
48: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.356 0.179 199.1
48: (ns/day) (hour/ns)
48: Performance: 8.219 2.920
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: NVE simulation: will use the initial temperature of 398.997 K for
48: determining the Verlet buffer size
48:
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
48: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.466 0.234 199.2
48: (ns/day) (hour/ns)
48: Performance: 6.275 3.825
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: NVE simulation: will use the initial temperature of 398.997 K for
48: determining the Verlet buffer size
48:
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
48: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.511 0.257 199.3
48: (ns/day) (hour/ns)
48: Performance: 5.725 4.192
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: NVE simulation: will use the initial temperature of 398.997 K for
48: determining the Verlet buffer size
48:
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
48: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.523 0.262 199.3
48: (ns/day) (hour/ns)
48: Performance: 5.597 4.288
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: NVE simulation: will use the initial temperature of 398.997 K for
48: determining the Verlet buffer size
48:
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
48: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.570 0.286 199.4
48: (ns/day) (hour/ns)
48: Performance: 5.133 4.675
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: NVE simulation: will use the initial temperature of 398.997 K for
48: determining the Verlet buffer size
48:
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
48: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.520 0.261 199.3
48: (ns/day) (hour/ns)
48: Performance: 5.632 4.261
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
48: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (26844 ms)
48: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.613 0.307 199.4
48: (ns/day) (hour/ns)
48: Performance: 4.782 5.019
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.494 0.249 198.8
48: (ns/day) (hour/ns)
48: Performance: 5.910 4.061
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.508 0.255 199.2
48: (ns/day) (hour/ns)
48: Performance: 5.758 4.168
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.353 0.178 198.8
48: (ns/day) (hour/ns)
48: Performance: 8.271 2.902
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.322 0.162 198.6
48: (ns/day) (hour/ns)
48: Performance: 9.053 2.651
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: Setting nstcalcenergy (100) equal to nstenergy (4)
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
48: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
48:
48: Using 2 MPI threads
48: Using 1 OpenMP thread per tMPI thread
48:
48:
48: NOTE: The number of threads is not equal to the number of (logical) cores
48: and the -pin option is set to auto: will not pin threads to cores.
48: This can lead to significant performance degradation.
48: Consider using -pin on (and -pinoffset in case you run multiple jobs).
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 16 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
48: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
48: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.341 0.172 198.3
48: (ns/day) (hour/ns)
48: Performance: 8.537 2.811
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
48: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (26881 ms)
48: [----------] 8 tests from PropagatorsWithConstraints/PeriodicActionsTest (216187 ms total)
48:
48: [----------] Global test environment tear-down
48: [==========] 27 tests from 3 test cases ran. (246737 ms total)
48: [ PASSED ] 27 tests.
48/52 Test #48: MdrunMpiCoordinationTestsTwoRanks ... Passed 246.83 sec
test 49
Start 49: GmxapiExternalInterfaceTests
49: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/gmxapi-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/GmxapiExternalInterfaceTests.xml"
49: Test timeout computed to be: 600
49: [==========] Running 9 tests from 2 test cases.
49: [----------] Global test environment set-up.
49: [----------] 8 tests from GmxApiTest
49: [ RUN ] GmxApiTest.ApiRunnerRestrainedMD
49: Setting the LD random seed to -1503343432
49: Generated 331705 of the 331705 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 331705 of the 331705 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Excluding 3 bonded neighbours molecule type 'methane'
49:
49: NOTE 1 [file spc_and_methane.top, line 33]:
49: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
49: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
49: the time step of 2.0e-03 ps.
49: Maybe you forgot to change the constraints mdp option.
49:
49: Number of degrees of freedom in T-Coupling group System is 18.00
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
49: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 2 OpenMP threads
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Water and methane'
49: 2 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
49: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.344 0.172 199.7
49: (ns/day) (hour/ns)
49: Performance: 2.936 8.175
49: [ OK ] GmxApiTest.ApiRunnerRestrainedMD (4351 ms)
49: [ RUN ] GmxApiTest.SystemConstruction
49: Setting the LD random seed to -470187208
49: Generated 331705 of the 331705 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 331705 of the 331705 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Excluding 3 bonded neighbours molecule type 'methane'
49:
49: NOTE 1 [file spc_and_methane.top, line 33]:
49: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
49: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
49: the time step of 2.0e-03 ps.
49: Maybe you forgot to change the constraints mdp option.
49:
49: Number of degrees of freedom in T-Coupling group System is 18.00
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_SystemConstruction_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 2 notes
49: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
49: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49: [ OK ] GmxApiTest.SystemConstruction (4176 ms)
49: [ RUN ] GmxApiTest.SaneVersionComparisons
49: [ OK ] GmxApiTest.SaneVersionComparisons (1 ms)
49: [ RUN ] GmxApiTest.VersionNamed0_1_Features
49: [ OK ] GmxApiTest.VersionNamed0_1_Features (0 ms)
49: [ RUN ] GmxApiTest.RunnerBasicMD
49: Setting the LD random seed to 118515563
49: Generated 331705 of the 331705 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 331705 of the 331705 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Excluding 3 bonded neighbours molecule type 'methane'
49:
49: NOTE 1 [file spc_and_methane.top, line 33]:
49: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
49: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
49: the time step of 2.0e-03 ps.
49: Maybe you forgot to change the constraints mdp option.
49:
49: Number of degrees of freedom in T-Coupling group System is 18.00
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
49: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 2 OpenMP threads
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Water and methane'
49: 2 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
49: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.414 0.207 199.7
49: (ns/day) (hour/ns)
49: Performance: 2.443 9.824
49: [ OK ] GmxApiTest.RunnerBasicMD (4368 ms)
49: [ RUN ] GmxApiTest.RunnerReinitialize
49: Setting the LD random seed to -1524992025
49: Generated 331705 of the 331705 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 331705 of the 331705 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Excluding 3 bonded neighbours molecule type 'methane'
49:
49: NOTE 1 [file spc_and_methane.top, line 33]:
49: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
49: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
49: the time step of 2.0e-03 ps.
49: Maybe you forgot to change the constraints mdp option.
49:
49: Number of degrees of freedom in T-Coupling group System is 18.00
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
49: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 2 OpenMP threads
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Water and methane'
49: 20 steps, 0.0 ps.
49:
49:
49: Received the remote INT/TERM signal, stopping within 50 steps
49:
49: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
49: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.509 0.255 199.7
49: (ns/day) (hour/ns)
49: Performance: 13.909 1.725
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
49: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 2 OpenMP threads
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Water and methane'
49: 20 steps, 0.0 ps.
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.452 0.227 199.4
49: (ns/day) (hour/ns)
49: Performance: 15.623 1.536
49: [ OK ] GmxApiTest.RunnerReinitialize (4656 ms)
49: [ RUN ] GmxApiTest.RunnerContinuedMD
49: Setting the LD random seed to -1352579651
49: Generated 331705 of the 331705 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 331705 of the 331705 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Excluding 3 bonded neighbours molecule type 'methane'
49:
49: NOTE 1 [file spc_and_methane.top, line 33]:
49: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
49: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
49: the time step of 2.0e-03 ps.
49: Maybe you forgot to change the constraints mdp option.
49:
49: Number of degrees of freedom in T-Coupling group System is 18.00
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerContinuedMD_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerContinuedMD.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
49: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 2 OpenMP threads
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Water and methane'
49: 10 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
49: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.492 0.246 199.7
49: (ns/day) (hour/ns)
49: Performance: 7.532 3.186
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerContinuedMD.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
49: Overriding nsteps with value passed on the command line: 20 steps, 0.0391 ps
49: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
49:
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 2 OpenMP threads
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Water and methane'
49: 20 steps, 0.0 ps.
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.430 0.216 199.3
49: (ns/day) (hour/ns)
49: Performance: 16.444 1.459
49: [ OK ] GmxApiTest.RunnerContinuedMD (4656 ms)
49: [ RUN ] GmxApiTest.ApiRunnerStopSignalClient
49: Setting the LD random seed to -1267299893
49: Generated 331705 of the 331705 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 331705 of the 331705 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Excluding 3 bonded neighbours molecule type 'methane'
49:
49: NOTE 1 [file spc_and_methane.top, line 33]:
49: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
49: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
49: the time step of 2.0e-03 ps.
49: Maybe you forgot to change the constraints mdp option.
49:
49: Number of degrees of freedom in T-Coupling group System is 18.00
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
49: Changing nstlist from 10 to 1, rlist from 1.041 to 1
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 2 OpenMP threads
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Water and methane'
49: 1 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
49: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.492 0.246 199.8
49: (ns/day) (hour/ns)
49: Performance: 1.370 17.515
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
49: Overriding nsteps with value passed on the command line: 2 steps, 0.00391 ps
49: Changing nstlist from 10 to 1, rlist from 1.041 to 1
49:
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 2 OpenMP threads
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Water and methane'
49: 2 steps, 0.0 ps.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.365 0.183 199.5
49: (ns/day) (hour/ns)
49: Performance: 1.847 12.993
49: [ OK ] GmxApiTest.ApiRunnerStopSignalClient (4587 ms)
49: [----------] 8 tests from GmxApiTest (26797 ms total)
49:
49: [----------] 1 test from GmxApiBasicTest
49: [ RUN ] GmxApiBasicTest.Status
49: [ OK ] GmxApiBasicTest.Status (0 ms)
49: [----------] 1 test from GmxApiBasicTest (0 ms total)
49:
49: [----------] Global test environment tear-down
49: [==========] 9 tests from 2 test cases ran. (26798 ms total)
49: [ PASSED ] 9 tests.
49/52 Test #49: GmxapiExternalInterfaceTests ........ Passed 26.90 sec
test 50
Start 50: GmxapiMpiTests
50: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/gmxapi-mpi-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/GmxapiMpiTests.xml"
50: Test timeout computed to be: 600
50: [==========] Running 9 tests from 2 test cases.
50: [----------] Global test environment set-up.
50: [----------] 8 tests from GmxApiTest
50: [ RUN ] GmxApiTest.ApiRunnerRestrainedMD
50: Setting the LD random seed to 1295266215
50: Generated 331705 of the 331705 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 331705 of the 331705 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Excluding 3 bonded neighbours molecule type 'methane'
50:
50: NOTE 1 [file spc_and_methane.top, line 33]:
50: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
50: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
50: the time step of 2.0e-03 ps.
50: Maybe you forgot to change the constraints mdp option.
50:
50: Number of degrees of freedom in T-Coupling group System is 18.00
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
50: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
50:
50: Using 1 MPI thread
50: Using 2 OpenMP threads
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Water and methane'
50: 2 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
50: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.498 0.249 199.8
50: (ns/day) (hour/ns)
50: Performance: 2.029 11.827
50: [ OK ] GmxApiTest.ApiRunnerRestrainedMD (4395 ms)
50: [ RUN ] GmxApiTest.SystemConstruction
50: Setting the LD random seed to -1148234029
50: Generated 331705 of the 331705 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 331705 of the 331705 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Excluding 3 bonded neighbours molecule type 'methane'
50:
50: NOTE 1 [file spc_and_methane.top, line 33]:
50: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
50: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
50: the time step of 2.0e-03 ps.
50: Maybe you forgot to change the constraints mdp option.
50:
50: Number of degrees of freedom in T-Coupling group System is 18.00
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_SystemConstruction_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 2 notes
50: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
50: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50: [ OK ] GmxApiTest.SystemConstruction (4143 ms)
50: [ RUN ] GmxApiTest.SaneVersionComparisons
50: [ OK ] GmxApiTest.SaneVersionComparisons (0 ms)
50: [ RUN ] GmxApiTest.VersionNamed0_1_Features
50: [ OK ] GmxApiTest.VersionNamed0_1_Features (0 ms)
50: [ RUN ] GmxApiTest.RunnerBasicMD
50: Setting the LD random seed to -19584071
50: Generated 331705 of the 331705 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 331705 of the 331705 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Excluding 3 bonded neighbours molecule type 'methane'
50:
50: NOTE 1 [file spc_and_methane.top, line 33]:
50: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
50: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
50: the time step of 2.0e-03 ps.
50: Maybe you forgot to change the constraints mdp option.
50:
50: Number of degrees of freedom in T-Coupling group System is 18.00
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
50: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
50:
50: Using 1 MPI thread
50: Using 2 OpenMP threads
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Water and methane'
50: 2 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
50: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.712 0.356 199.8
50: (ns/day) (hour/ns)
50: Performance: 1.422 16.884
50: [ OK ] GmxApiTest.RunnerBasicMD (4500 ms)
50: [ RUN ] GmxApiTest.RunnerReinitialize
50: Setting the LD random seed to -1409184819
50: Generated 331705 of the 331705 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 331705 of the 331705 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Excluding 3 bonded neighbours molecule type 'methane'
50:
50: NOTE 1 [file spc_and_methane.top, line 33]:
50: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
50: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
50: the time step of 2.0e-03 ps.
50: Maybe you forgot to change the constraints mdp option.
50:
50: Number of degrees of freedom in T-Coupling group System is 18.00
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
50: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
50:
50: Using 1 MPI thread
50: Using 2 OpenMP threads
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Water and methane'
50: 20 steps, 0.0 ps.
50:
50:
50: Received the remote INT/TERM signal, stopping within 50 steps
50:
50: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
50: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.595 0.298 199.7
50: (ns/day) (hour/ns)
50: Performance: 11.896 2.018
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
50: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
50:
50: Using 1 MPI thread
50: Using 2 OpenMP threads
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Water and methane'
50: 20 steps, 0.0 ps.
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.563 0.282 199.6
50: (ns/day) (hour/ns)
50: Performance: 12.551 1.912
50: [ OK ] GmxApiTest.RunnerReinitialize (4755 ms)
50: [ RUN ] GmxApiTest.RunnerContinuedMD
50: Setting the LD random seed to -938469221
50: Generated 331705 of the 331705 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 331705 of the 331705 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Excluding 3 bonded neighbours molecule type 'methane'
50:
50: NOTE 1 [file spc_and_methane.top, line 33]:
50: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
50: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
50: the time step of 2.0e-03 ps.
50: Maybe you forgot to change the constraints mdp option.
50:
50: Number of degrees of freedom in T-Coupling group System is 18.00
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerContinuedMD_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerContinuedMD.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
50: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
50:
50: Using 1 MPI thread
50: Using 2 OpenMP threads
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Water and methane'
50: 10 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
50: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.739 0.370 199.8
50: (ns/day) (hour/ns)
50: Performance: 5.019 4.781
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerContinuedMD.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
50: Overriding nsteps with value passed on the command line: 20 steps, 0.0391 ps
50: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
50:
50:
50: Using 1 MPI thread
50: Using 2 OpenMP threads
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Water and methane'
50: 20 steps, 0.0 ps.
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.586 0.294 199.5
50: (ns/day) (hour/ns)
50: Performance: 12.071 1.988
50: [ OK ] GmxApiTest.RunnerContinuedMD (4812 ms)
50: [ RUN ] GmxApiTest.ApiRunnerStopSignalClient
50: Setting the LD random seed to -1535386312
50: Generated 331705 of the 331705 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 331705 of the 331705 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Excluding 3 bonded neighbours molecule type 'methane'
50:
50: NOTE 1 [file spc_and_methane.top, line 33]:
50: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
50: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
50: the time step of 2.0e-03 ps.
50: Maybe you forgot to change the constraints mdp option.
50:
50: Number of degrees of freedom in T-Coupling group System is 18.00
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
50: Changing nstlist from 10 to 1, rlist from 1.041 to 1
50:
50: Using 1 MPI thread
50: Using 2 OpenMP threads
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Water and methane'
50: 1 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
50: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.560 0.280 199.8
50: (ns/day) (hour/ns)
50: Performance: 1.204 19.930
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2020.3-Raspbian-2020.3-1 (double precision)
50: Overriding nsteps with value passed on the command line: 2 steps, 0.00391 ps
50: Changing nstlist from 10 to 1, rlist from 1.041 to 1
50:
50:
50: Using 1 MPI thread
50: Using 2 OpenMP threads
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Water and methane'
50: 2 steps, 0.0 ps.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.387 0.194 199.6
50: (ns/day) (hour/ns)
50: Performance: 1.741 13.782
50: [ OK ] GmxApiTest.ApiRunnerStopSignalClient (4621 ms)
50: [----------] 8 tests from GmxApiTest (27228 ms total)
50:
50: [----------] 1 test from GmxApiBasicTest
50: [ RUN ] GmxApiBasicTest.Status
50: [ OK ] GmxApiBasicTest.Status (0 ms)
50: [----------] 1 test from GmxApiBasicTest (0 ms total)
50:
50: [----------] Global test environment tear-down
50: [==========] 9 tests from 2 test cases ran. (27228 ms total)
50: [ PASSED ] 9 tests.
50/52 Test #50: GmxapiMpiTests ...................... Passed 27.31 sec
test 51
Start 51: GmxapiInternalInterfaceTests
51: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/workflow-details-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/GmxapiInternalInterfaceTests.xml"
51: Test timeout computed to be: 600
51: [==========] Running 2 tests from 1 test case.
51: [----------] Global test environment set-up.
51: [----------] 2 tests from GmxApiTest
51: [ RUN ] GmxApiTest.BuildApiWorkflowImpl
51: Setting the LD random seed to 849179778
51: Generated 331705 of the 331705 non-bonded parameter combinations
51: Generating 1-4 interactions: fudge = 0.5
51: Generated 331705 of the 331705 1-4 parameter combinations
51: Excluding 2 bonded neighbours molecule type 'SOL'
51: Excluding 3 bonded neighbours molecule type 'methane'
51:
51: NOTE 1 [file spc_and_methane.top, line 33]:
51: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
51: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
51: the time step of 2.0e-03 ps.
51: Maybe you forgot to change the constraints mdp option.
51:
51: Number of degrees of freedom in T-Coupling group System is 18.00
51:
51: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests/Testing/Temporary/GmxApiTest_BuildApiWorkflowImpl_input.mdp]:
51: You are using a plain Coulomb cut-off, which might produce artifacts.
51: You might want to consider using PME electrostatics.
51:
51:
51:
51: There were 2 notes
51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
51: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
51: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
51: Note that mdrun will redetermine rlist based on the actual pair-list setup
51: This run will generate roughly 0 Mb of data
51: [ OK ] GmxApiTest.BuildApiWorkflowImpl (4021 ms)
51: [ RUN ] GmxApiTest.CreateApiWorkflow
51: Setting the LD random seed to -1482878383
51: Generated 331705 of the 331705 non-bonded parameter combinations
51: Generating 1-4 interactions: fudge = 0.5
51: Generated 331705 of the 331705 1-4 parameter combinations
51: Excluding 2 bonded neighbours molecule type 'SOL'
51: Excluding 3 bonded neighbours molecule type 'methane'
51:
51: NOTE 1 [file spc_and_methane.top, line 33]:
51: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
51: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
51: the time step of 2.0e-03 ps.
51: Maybe you forgot to change the constraints mdp option.
51:
51: Number of degrees of freedom in T-Coupling group System is 18.00
51:
51: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests/Testing/Temporary/GmxApiTest_CreateApiWorkflow_input.mdp]:
51: You are using a plain Coulomb cut-off, which might produce artifacts.
51: You might want to consider using PME electrostatics.
51:
51:
51:
51: There were 2 notes
51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
51: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
51: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
51: Note that mdrun will redetermine rlist based on the actual pair-list setup
51: This run will generate roughly 0 Mb of data
51: [ OK ] GmxApiTest.CreateApiWorkflow (4139 ms)
51: [----------] 2 tests from GmxApiTest (8161 ms total)
51:
51: [----------] Global test environment tear-down
51: [==========] 2 tests from 1 test case ran. (8162 ms total)
51: [ PASSED ] 2 tests.
51/52 Test #51: GmxapiInternalInterfaceTests ........ Passed 8.24 sec
test 52
Start 52: GmxapiInternalsMpiTests
52: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/workflow-details-mpi-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/GmxapiInternalsMpiTests.xml"
52: Test timeout computed to be: 600
52: [==========] Running 2 tests from 1 test case.
52: [----------] Global test environment set-up.
52: [----------] 2 tests from GmxApiTest
52: [ RUN ] GmxApiTest.BuildApiWorkflowImpl
52: Setting the LD random seed to -1484101187
52: Generated 331705 of the 331705 non-bonded parameter combinations
52: Generating 1-4 interactions: fudge = 0.5
52: Generated 331705 of the 331705 1-4 parameter combinations
52: Excluding 2 bonded neighbours molecule type 'SOL'
52: Excluding 3 bonded neighbours molecule type 'methane'
52:
52: NOTE 1 [file spc_and_methane.top, line 33]:
52: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
52: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
52: the time step of 2.0e-03 ps.
52: Maybe you forgot to change the constraints mdp option.
52:
52: Number of degrees of freedom in T-Coupling group System is 18.00
52:
52: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests/Testing/Temporary/GmxApiTest_BuildApiWorkflowImpl_input.mdp]:
52: You are using a plain Coulomb cut-off, which might produce artifacts.
52: You might want to consider using PME electrostatics.
52:
52:
52:
52: There were 2 notes
52: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
52: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
52: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
52: Note that mdrun will redetermine rlist based on the actual pair-list setup
52: This run will generate roughly 0 Mb of data
52: [ OK ] GmxApiTest.BuildApiWorkflowImpl (4022 ms)
52: [ RUN ] GmxApiTest.CreateApiWorkflow
52: Setting the LD random seed to 773466435
52: Generated 331705 of the 331705 non-bonded parameter combinations
52: Generating 1-4 interactions: fudge = 0.5
52: Generated 331705 of the 331705 1-4 parameter combinations
52: Excluding 2 bonded neighbours molecule type 'SOL'
52: Excluding 3 bonded neighbours molecule type 'methane'
52:
52: NOTE 1 [file spc_and_methane.top, line 33]:
52: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
52: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
52: the time step of 2.0e-03 ps.
52: Maybe you forgot to change the constraints mdp option.
52:
52: Number of degrees of freedom in T-Coupling group System is 18.00
52:
52: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests/Testing/Temporary/GmxApiTest_CreateApiWorkflow_input.mdp]:
52: You are using a plain Coulomb cut-off, which might produce artifacts.
52: You might want to consider using PME electrostatics.
52:
52:
52:
52: There were 2 notes
52: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
52: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
52: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
52: Note that mdrun will redetermine rlist based on the actual pair-list setup
52: This run will generate roughly 0 Mb of data
52: [ OK ] GmxApiTest.CreateApiWorkflow (4135 ms)
52: [----------] 2 tests from GmxApiTest (8157 ms total)
52:
52: [----------] Global test environment tear-down
52: [==========] 2 tests from 1 test case ran. (8157 ms total)
52: [ PASSED ] 2 tests.
52/52 Test #52: GmxapiInternalsMpiTests ............. Passed 8.24 sec
100% tests passed, 0 tests failed out of 52
Label Time Summary:
GTest = 888.13 sec*proc (52 tests)
IntegrationTest = 328.20 sec*proc (9 tests)
MpiTest = 594.13 sec*proc (8 tests)
SlowTest = 485.00 sec*proc (2 tests)
UnitTest = 74.93 sec*proc (41 tests)
Total Test time (real) = 888.44 sec
touch build-basic
dh_testdir
/usr/bin/make -j4 -C build/mpich
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make[2]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
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cd /<<PKGBUILDDIR>>/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/mpich /<<PKGBUILDDIR>>/build/mpich/src/gromacs /<<PKGBUILDDIR>>/build/mpich/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/mpich /<<PKGBUILDDIR>>/build/mpich/src/gromacs /<<PKGBUILDDIR>>/build/mpich/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/build/mpich /<<PKGBUILDDIR>>/build/mpich /<<PKGBUILDDIR>>/build/mpich/CMakeFiles/release-version-info.dir/DependInfo.cmake --color=
cd /<<PKGBUILDDIR>>/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/selection /<<PKGBUILDDIR>>/build/mpich /<<PKGBUILDDIR>>/build/mpich/src/gromacs/selection /<<PKGBUILDDIR>>/build/mpich/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake --color=
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make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>> && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2020.3-Raspbian-2020.3-1 -D PROJECT_SOURCE_DIR=/<<PKGBUILDDIR>> -D DIRECTORIES_TO_CHECKSUM=src:python_packaging -D VERSION_CMAKEIN=/<<PKGBUILDDIR>>/build/mpich/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/<<PKGBUILDDIR>>/build/mpich/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Raspbian-2020.3-1 -P /<<PKGBUILDDIR>>/cmake/gmxGenerateVersionInfoRelease.cmake
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make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/errhandler.cpp
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cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/selection && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -std=c++14 -o CMakeFiles/scanner.dir/parser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/parser.cpp
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make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/bwlzh.c
[ 0%] Built target release-version-info
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cd /<<PKGBUILDDIR>>/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/mpich /<<PKGBUILDDIR>>/build/mpich/src/gromacs /<<PKGBUILDDIR>>/build/mpich/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color=
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make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -std=c++14 -o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -c /<<PKGBUILDDIR>>/src/external/lmfit/lmmin.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/tmpi_malloc.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/atomic.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/lock.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/pthreads.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/bwt.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/system_error.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/system_error.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/coder.c
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/usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend
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cd /<<PKGBUILDDIR>>/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/linearalgebra /<<PKGBUILDDIR>>/build/mpich /<<PKGBUILDDIR>>/build/mpich/src/gromacs/linearalgebra /<<PKGBUILDDIR>>/build/mpich/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake --color=
Scanning dependencies of target linearalgebra
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cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/linearalgebra && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/eigensolver.cpp
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[ 2%] Built target lmfit_objlib
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/dict.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/fixpoint.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/linearalgebra && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/gmx_arpack.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/huffman.c
/usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/modularsimulator /<<PKGBUILDDIR>>/build/mpich /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake --color=
Scanning dependencies of target modularsimulator
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
/usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/checkpointhelper.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/huffmem.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/lz77.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/compositesimulatorelement.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/merge_sort.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/mtf.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/rle.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/tng_compress.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/linearalgebra && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/matrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/matrix.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/constraintelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/constraintelement.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/linearalgebra && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/nrjac.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/nrjac.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/vals16.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/warnmalloc.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/widemuldiv.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/xtc2.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/linearalgebra && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/sparsematrix.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/selection && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -std=c++14 -o CMakeFiles/scanner.dir/scanner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/scanner.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/domdechelper.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/domdechelper.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
[ 2%] Built target linearalgebra
/usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs /<<PKGBUILDDIR>>/build/mpich /<<PKGBUILDDIR>>/build/mpich/src/programs /<<PKGBUILDDIR>>/build/mpich/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun_objlib
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
/usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich/src/programs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/mdrun.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/energyelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/energyelement.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
[ 2%] Built target scanner
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/forceelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/forceelement.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/xtc3.c
cd /<<PKGBUILDDIR>>/build/mpich/src/programs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/nonbonded_bench.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/freeenergyperturbationelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/freeenergyperturbationelement.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/modularsimulator.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/lib/tng_io.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/parrinellorahmanbarostat.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
[ 2%] Built target mdrun_objlib
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/pmeloadbalancehelper.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/propagator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/propagator.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/shellfcelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/shellfcelement.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/signallers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/signallers.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/topologyholder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/topologyholder.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/trajectoryelement.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/vrescalethermostat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/vrescalethermostat.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/lib/md5.c
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
[ 5%] Built target modularsimulator
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
[ 8%] Built target tng_io_obj
/usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/<<PKGBUILDDIR>>/build/mpich/VersionInfo.cmake -D VERSION_CMAKEIN=/<<PKGBUILDDIR>>/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI= -D GMX_RELEASE_HASH= -D GMX_SOURCE_HASH= -P /<<PKGBUILDDIR>>/cmake/gmxConfigureVersionInfo.cmake
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp
cd /<<PKGBUILDDIR>>/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/mpich /<<PKGBUILDDIR>>/build/mpich/src/gromacs /<<PKGBUILDDIR>>/build/mpich/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color=
Scanning dependencies of target libgromacs
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
/usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/alignedallocator.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/any.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/any.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/basenetwork.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/baseversion.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/binaryinformation.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/compare.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/compare.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/coolstuff.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/cstringutil.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/datafilefinder.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/directoryenumerator.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/errorcodes.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/errorformat.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/exceptions.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/fatalerror.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/fileredirector.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/filestream.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/filestream.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/futil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/futil.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/gmxassert.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/gmxassert.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/gmxomp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/gmxomp.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/ikeyvaluetreeerror.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/ikeyvaluetreeerror.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/init.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/init.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/inmemoryserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/inmemoryserializer.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/int64_to_int.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/int64_to_int.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/keyvaluetree.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/keyvaluetree.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/keyvaluetreemdpwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/keyvaluetreemdpwriter.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/keyvaluetreeserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/keyvaluetreeserializer.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/keyvaluetreetransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/keyvaluetreetransform.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/logger.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/logger.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/loggerbuilder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/loggerbuilder.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/messagestringcollector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/messagestringcollector.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/mpiinplacebuffers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/mpiinplacebuffers.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/niceheader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/niceheader.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/path.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/path.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/physicalnodecommunicator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/physicalnodecommunicator.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/pleasecite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/pleasecite.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/programcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/programcontext.cpp
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cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/strconvert.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/strconvert.cpp
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cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/stringstream.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/stringstream.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/stringutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/sysinfo.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/sysinfo.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/textreader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/textreader.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/textwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/textwriter.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/txtdump.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/atomdata.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_setup.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_system.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/gridset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernel_common.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernel_common.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kerneldispatch.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_ref.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_ref_prune.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_prune.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_prune.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm_geometry.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm_setup.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist_tuning.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairlistparams.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlistparams.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairlistset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlistset.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairsearch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairsearch.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/prunekerneldispatch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/prunekerneldispatch.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpcontext.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpmodule.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpwriter.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineinit.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinemodule.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodulemanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinemodulemanager.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlineoptionsmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineoptionsmodule.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineparser.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlineprogramcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineprogramcontext.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/filenm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/pargs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/shellcompletions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/shellcompletions.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/viewit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/viewit.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/atomdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/atomdistribution.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/box.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/cellsizes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/cellsizes.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/collect.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/distribute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/dlb.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/dlbtiming.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_constraints.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_network.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_setup.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_specatomcomm.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_topology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_topology.cpp
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cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/dump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/dump.cpp
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cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/gpuhaloexchange_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/gpuhaloexchange_impl.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/localatomset.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/localatomsetdata.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/localatomsetmanager.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/mdsetup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/mdsetup.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/partition.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/redistribute.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/utility.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/utility.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/3dtransforms.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/coordinatetransformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/densityfit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/densityfit.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/densityfittingforce.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/densityfittingforce.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/do_fit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/do_fit.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/exponentialmovingaverage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/exponentialmovingaverage.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/functions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/functions.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/gausstransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/gausstransform.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/invertmatrix.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/units.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/units.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/utilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/utilities.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/veccompare.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/veccompare.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/vecdump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/vecdump.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/df_history.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/group.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/iforceprovider.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -Wno-class-memaccess -o CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/inputrec.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/md_enums.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/observableshistory.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpformat.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:40:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:40:
/usr/include/c++/9/bits/stl_vector.h: In function 'void init_gtc_state(t_state*, int, int, int)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpmanager.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helptopic.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpwritercontext.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/rstparser.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/boxutilities.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/mshift.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc_simd.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcenums.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/rmpbc.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/random/seed.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/seed.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tabulatednormaldistribution.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/forcetable.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp: In constructor 'gmx::CubicSplineTable::CubicSplineTable(std::initializer_list<gmx::NumericalSplineTableInput>, const std::pair<float, float>&, real)':
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp:383:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
383 | CubicSplineTable::CubicSplineTable(std::initializer_list<NumericalSplineTableInput> numericalInputList,
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp:383:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp: In constructor 'gmx::QuadraticSplineTable::QuadraticSplineTable(std::initializer_list<gmx::NumericalSplineTableInput>, const std::pair<float, float>&, real)':
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp:367:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
367 | QuadraticSplineTable::QuadraticSplineTable(std::initializer_list<NumericalSplineTableInput> numericalInputList,
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp:170:99: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
170 | std::vector<double> thirdDerivative(internal::vectorSecondDerivative(derivative, inputSpacing));
| ^
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/cyclecounter.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/wallcycle.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/walltime_accounting.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atomprop.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'real gmx::internal::findSmallestQuotientOfFunctionAndSecondDerivative(gmx::ArrayRef<const double>, double, const std::pair<float, float>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:211:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
211 | real findSmallestQuotientOfFunctionAndSecondDerivative(ArrayRef<const double> function,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'real gmx::internal::findSmallestQuotientOfFunctionAndThirdDerivative(gmx::ArrayRef<const double>, double, const std::pair<float, float>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:291:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
291 | real findSmallestQuotientOfFunctionAndThirdDerivative(ArrayRef<const double> function,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'std::vector<double> gmx::internal::vectorSecondDerivative(gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:310:21: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
310 | std::vector<double> vectorSecondDerivative(ArrayRef<const double> f, double spacing)
| ^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'void gmx::internal::throwUnlessDerivativeIsConsistentWithFunction(gmx::ArrayRef<const double>, gmx::ArrayRef<const double>, double, const std::pair<float, float>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:112:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
112 | void throwUnlessDerivativeIsConsistentWithFunction(ArrayRef<const double> function,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:112:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/atoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atoms.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atomsbuilder.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/block.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/block.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/exclusionblocks.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/forcefieldparameters.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/idef.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/idef.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/ifunc.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/index.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/index.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/invblock.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/invblock.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/mtop_util.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/residuetypes.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/symtab.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/symtab.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/topology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/topology.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/topsort.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/topsort.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/swap/swapcoords.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/essentialdynamics/edsam.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pulling/output.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/output.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pulling/pull.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pulling/pull_rotation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pull_rotation.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:39:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_pull_group&, gmx::LocalAtomSet, const bool&}; _Tp = pull_group_work_t; _Alloc = std::allocator<pull_group_work_t>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' {aka '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_pull_coord&}; _Tp = pull_coord_work_t; _Alloc = std::allocator<pull_coord_work_t>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pull_coord_work_t>::iterator' {aka '__gnu_cxx::__normal_iterator<pull_coord_work_t*, std::vector<pull_coord_work_t> >'} changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In function 'pull_t* init_pull(FILE*, const pull_params_t*, const t_inputrec*, const gmx_mtop_t*, const t_commrec*, gmx::LocalAtomSetManager*, real)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pull_coord_work_t*, std::vector<pull_coord_work_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2280:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' {aka '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >'} changed in GCC 7.1
2280 | }
| ^
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/awh.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/awh.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/gmxlib/network.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:45:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/gmxlib/network.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:45:
/usr/include/c++/9/bits/stl_vector.h: In function 'void allocStatePrevStepPullCom(t_state*, const pull_t*)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/bias.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/biasparams.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biasparams.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/biasparams.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/awh/biasparams.cpp:47:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp: In member function 'void gmx::Bias::updateForceCorrelationGrid(gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:386:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
386 | void Bias::updateForceCorrelationGrid(gmx::ArrayRef<const double> probWeightNeighbor, double t)
| ^~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:406:45: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
406 | state_.calcUmbrellaForceAndPotential(dimParams_, grid_, indexNeighbor, forceFromNeighbor);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:70:
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationgrid.h:104:37: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
104 | tensors_[pointIndex].addData(weight, data, blockLengthMeasure == BlockLengthMeasure::Weight, t);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In constructor 'gmx::BiasParams::BiasParams(const gmx::AwhParams&, const gmx::AwhBiasParams&, const std::vector<gmx::DimParams>&, double, double, gmx::BiasParams::DisableUpdateSkips, int, const std::vector<gmx::GridAxis>&, int)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp: In member function 'gmx::ArrayRef<const double> gmx::Bias::calcForceAndUpdateBias(const double*, double*, double*, const t_commrec*, const gmx_multisim_t*, double, int64_t, int64_t, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:144:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
144 | updateForceCorrelationGrid(probWeightNeighbor, t);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
162 | state_.calcConvolvedForce(dimParams_, grid_, probWeightNeighbor, tempForce_, biasForce_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:172:57: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
172 | potential = state_.calcUmbrellaForceAndPotential(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
173 | dimParams_, grid_, coordState.umbrellaGridpoint(), biasForce_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
182 | double newPotential = state_.moveUmbrella(dimParams_, grid_, probWeightNeighbor,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
183 | biasForce_, step, seed, params_.biasIndex);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/biassharing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biassharing.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.cpp:47:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, const double&, const double&}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >'} changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/biasstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::Bias, std::vector<int, std::allocator<int> >&}; _Tp = gmx::BiasCoupledToSystem; _Alloc = std::allocator<gmx::BiasCoupledToSystem>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BiasCoupledToSystem>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BiasCoupledToSystem*, std::vector<gmx::BiasCoupledToSystem> >'} changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In constructor 'gmx::Awh::Awh(FILE*, const t_inputrec&, const t_commrec*, const gmx_multisim_t*, const gmx::AwhParams&, const string&, pull_t*)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BiasCoupledToSystem*, std::vector<gmx::BiasCoupledToSystem> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/biaswriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biaswriter.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/coordstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/coordstate.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In function 'void gmx::{anonymous}::updateTargetDistribution(gmx::ArrayRef<gmx::PointState>, const gmx::BiasParams&)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:292:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::PointState>' changed in GCC 7.1
292 | void updateTargetDistribution(gmx::ArrayRef<PointState> pointState, const BiasParams& params)
| ^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'double gmx::BiasState::calcUmbrellaForceAndPotential(const std::vector<gmx::DimParams>&, const gmx::Grid&, int, gmx::ArrayRef<double>) const':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:416:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
416 | double BiasState::calcUmbrellaForceAndPotential(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::calcConvolvedForce(const std::vector<gmx::DimParams>&, const gmx::Grid&, gmx::ArrayRef<const double>, gmx::ArrayRef<double>, gmx::ArrayRef<double>) const':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:437:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
437 | void BiasState::calcConvolvedForce(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:437:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:437:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'double gmx::BiasState::moveUmbrella(const std::vector<gmx::DimParams>&, const gmx::Grid&, gmx::ArrayRef<const double>, gmx::ArrayRef<double>, int64_t, int64_t, int)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:467:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
467 | double BiasState::moveUmbrella(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:467:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:476:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
476 | coordState_.sampleUmbrellaGridpoint(grid, coordState_.gridpointIndex(), probWeightNeighbor,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
477 | step, seed, indexSeed);
| ~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:476:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::sampleProbabilityWeights(const gmx::Grid&, gmx::ArrayRef<const double>)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1233:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1233 | void BiasState::sampleProbabilityWeights(const Grid& grid, gmx::ArrayRef<const double> probWeightNeighbor)
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::sampleCoordAndPmf(const gmx::Grid&, gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1287:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1287 | void BiasState::sampleCoordAndPmf(const Grid& grid, gmx::ArrayRef<const double> probWeightNeighbor, double convolvedBias)
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/coordstate.cpp: In member function 'void gmx::CoordState::sampleUmbrellaGridpoint(const gmx::Grid&, int, gmx::ArrayRef<const double>, int64_t, int64_t, int)':
/<<PKGBUILDDIR>>/src/gromacs/awh/coordstate.cpp:129:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
129 | void CoordState::sampleUmbrellaGridpoint(const Grid& grid,
| ^~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/correlationgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/correlationgrid.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/correlationhistory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/correlationhistory.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::updateFreeEnergyAndAddSamplesToHistogram(const std::vector<gmx::DimParams>&, const gmx::Grid&, const gmx::BiasParams&, const t_commrec*, const gmx_multisim_t*, double, int64_t, FILE*, std::vector<int>*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
1072 | double newHistogramSize = histogramSize_.newHistogramSize(params, t, detectedCovering, points_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1073 | weightSumCovering_, fplog);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/correlationtensor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/grid.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/histogramsize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp: In member function 'void gmx::CorrelationTensor::addData(double, gmx::ArrayRef<const double>, bool, double)':
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp:229:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
229 | void CorrelationTensor::addData(double weight, gmx::ArrayRef<const double> data, bool blockLengthInWeight, double t)
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp:229:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp:47:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {int&, double}; _Tp = gmx::CorrelationBlockData; _Alloc = std::allocator<gmx::CorrelationBlockData>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::CorrelationBlockData>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::CorrelationBlockData*, std::vector<gmx::CorrelationBlockData> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In constructor 'gmx::CorrelationTensor::CorrelationTensor(int, int, double)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::CorrelationBlockData*, std::vector<gmx::CorrelationBlockData> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/pointstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/pointstate.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp: In member function 'double gmx::HistogramSize::newHistogramSizeInitialStage(const gmx::BiasParams&, double, bool, gmx::ArrayRef<double>, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp:77:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
77 | double HistogramSize::newHistogramSizeInitialStage(const BiasParams& params,
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp: In member function 'double gmx::HistogramSize::newHistogramSize(const gmx::BiasParams&, double, bool, const std::vector<gmx::PointState>&, gmx::ArrayRef<double>, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp:209:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
209 | double HistogramSize::newHistogramSize(const BiasParams& params,
| ^~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/read_params.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/read_params.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/simd/support.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/support.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/dimparams.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/awh/grid.h:60,
from /<<PKGBUILDDIR>>/src/gromacs/awh/grid.cpp:47:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, double&, double&, double&}; _Tp = gmx::GridAxis; _Alloc = std::allocator<gmx::GridAxis>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::GridAxis>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In constructor 'gmx::Grid::Grid(const std::vector<gmx::DimParams>&, const gmx::AwhDimParams*)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&, const double&, double, int&}; _Tp = gmx::GridAxis; _Alloc = std::allocator<gmx::GridAxis>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::GridAxis>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In function 'void gmx::mapGridToDataGrid(std::vector<int>*, const double* const*, int, const string&, const gmx::Grid&, const string&)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/imd/imd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/imd/imd.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/imd/imdsocket.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxlib/conformation_utilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/conformation_utilities.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxlib/network.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/network.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxlib/nrnb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nrnb.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_free_energy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_free_energy.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/boxdeformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/boxdeformation.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/broadcaststructs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/calc_verletbuf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/calc_verletbuf.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/calcmu.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/calcmu.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/calcvir.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/calcvir.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/checkpointhandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/checkpointhandler.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/compute_io.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/compute_io.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/constr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/constraintrange.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/coupling.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/dispersioncorrection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/ebin.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/enerdata_utils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/energyoutput.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/energyoutput.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/expanded.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/force.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/forcerec.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/gmx_omp_nthreads.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/groupcoord.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/forcerec.cpp: In function 'void __static_initialization_and_destruction_0(int, int)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/forcerec.cpp:103:16: warning: ignoring return value of 'char* getenv(const char*)', declared with attribute warn_unused_result [-Wunused-result]
103 | (getenv("GMX_GPU_PME_PP_COMMS") != nullptr) && GMX_THREAD_MPI && (GMX_GPU == GMX_GPU_CUDA);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/md_support.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdebin_bar.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/membed.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/nsgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nsgrid.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/perf_est.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qm_gamess.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_gamess.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qm_gaussian.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_gaussian.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qm_mopac.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_mopac.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qm_orca.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_orca.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qmmm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qmmm.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/resethandler.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/rf_util.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/settle.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/sighandler.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/simulationsignal.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/splitter.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/stat.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/stophandler.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tgroup.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/trajectory_writing.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/update.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/update_constrain_cuda_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/update_constrain_cuda_impl.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update_constrain_cuda_impl.cpp: In member function 'void gmx::UpdateConstrainCuda::integrate(GpuEventSynchronizer*, real, bool, bool, real (*)[3], bool, gmx::ArrayRef<const t_grp_tcstat>, bool, float, const real (*)[3])':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update_constrain_cuda_impl.cpp:70:6: note: parameter passing for argument of type 'gmx::ArrayRef<const t_grp_tcstat>' changed in GCC 7.1
70 | void UpdateConstrainCuda::integrate(GpuEventSynchronizer* /* fReadyOnDevice */,
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroups.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/vcm.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/wall.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfittingamplitudelookup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingamplitudelookup.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfittingforceprovider.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingforceprovider.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfittingoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingoptions.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfittingoutputprovider.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingoutputprovider.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfittingparameters.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingparameters.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/electricfield.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/electricfield.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/bonded.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/bonded.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/disre.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/disre.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/gpubonded_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/gpubonded_impl.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/listed_forces.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/listed_forces.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/listed_internal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/listed_internal.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/manage_threading.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/manage_threading.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/orires.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/orires.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/pairs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/pairs.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/position_restraints.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/position_restraints.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/restcbt.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/restcbt.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/calculate_spline_moduli.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/calculate_spline_moduli.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/ewald.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/ewald.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/ewald_utils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/ewald_utils.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/long_range_correction.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/long_range_correction.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_gather.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_gather.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_grid.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_load_balancing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_only.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_pp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_pp.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/forcerec.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp:47:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const pme_setup_t&}; _Tp = pme_setup_t; _Alloc = std::allocator<pme_setup_t>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pme_setup_t>::iterator' {aka '__gnu_cxx::__normal_iterator<pme_setup_t*, std::vector<pme_setup_t> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/forcerec.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp:47:
/usr/include/c++/9/bits/stl_vector.h: In function 'void pme_load_balance(pme_load_balancing_t*, t_commrec*, FILE*, FILE*, const gmx::MDLogger&, const t_inputrec&, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<float> >, double, interaction_const_t*, nonbonded_verlet_t*, gmx_pme_t**, int64_t)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pme_setup_t*, std::vector<pme_setup_t> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp: In function 'void __static_initialization_and_destruction_0(int, int)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp:104:16: warning: ignoring return value of 'char* getenv(const char*)', declared with attribute warn_unused_result [-Wunused-result]
104 | (getenv("GMX_GPU_PME_PP_COMMS") != nullptr) && GMX_THREAD_MPI && (GMX_GPU == GMX_GPU_CUDA);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_redistribute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_redistribute.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_solve.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_solve.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_spline_work.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_spline_work.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_spread.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_spread.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_gpu_program.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_pp_comm_gpu_impl.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_coordinate_receiver_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_coordinate_receiver_gpu_impl.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_force_sender_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_force_sender_gpu_impl.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_gpu_program_impl.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fft/calcgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/calcgrid.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fft/fft.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/fft.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fft/fft5d.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/fft5d.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fft/parallel_3dfft.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/parallel_3dfft.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fft/fft_fftw3.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/fft_fftw3.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/clfftinitializer.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gpu_utils/hostallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/gpu_utils.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gpu_utils/gpu_testutils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/gpu_testutils.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/cpuinfo.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/cpuinfo.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/detecthardware.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/detecthardware.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/gpu_hw_info.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/gpu_hw_info.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/hardwaretopology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/hardwaretopology.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/printhardware.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/printhardware.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/identifyavx512fmaunits.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/identifyavx512fmaunits.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/legacymdrunoptions.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/legacysimulator.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/md.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/mdmodules.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/mdmodules.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/replicaexchange.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp: In member function 'void gmx::LegacySimulator::do_md()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1293:34: note: parameter passing for argument of type 'gmx::ArrayRef<const t_grp_tcstat>' changed in GCC 7.1
1293 | integrator->integrate(stateGpu->getForcesReadyOnDeviceEvent(
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1294 | AtomLocality::Local, runScheduleWork->stepWork.useGpuFBufferOps),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1295 | ir->delta_t, true, bCalcVir, shake_vir, doTemperatureScaling,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1296 | ekind->tcstat, doParrinelloRahman, ir->nstpcouple * ir->delta_t, M);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/rerun.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/shellfc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/simulationcontext.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/handlerestart.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/logging.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/multisim.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/printtime.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/threadaffinity.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/abstractoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/abstractoption.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/abstractsection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/abstractsection.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/basicoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/behaviorcollection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/behaviorcollection.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/filenameoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/filenameoption.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/filenameoptionmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/filenameoptionmanager.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/options.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/options.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/optionsassigner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/optionsassigner.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/optionsection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/optionsection.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/optionsvisitor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/optionsvisitor.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/timeunitmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/timeunitmanager.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/treesupport.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/treesupport.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/restraint/manager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/restraint/manager.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/restraint/restraintmdmodule.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual void gmx::DoubleOptionStorage::processSetValues(gmx::OptionStorageTemplate<double>::ValueList*)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/decidegpuusage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/decidegpuusage.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/decidesimulationworkload.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/decidesimulationworkload.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/9/bits/stl_vector.h: In member function 'void gmx::OptionStorageTemplate<T>::addValue(const T&) [with T = double]':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreNull<T>::append(const T&) [with T = double]':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreVector<T>::append(const T&) [with T = double]':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<long long int, std::allocator<long long int> >::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/9/bits/stl_vector.h: In member function 'void gmx::OptionStorageTemplate<T>::addValue(const T&) [with T = long long int]':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreVector<T>::append(const T&) [with T = long long int]':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreNull<T>::append(const T&) [with T = long long int]':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/findallgputasks.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/findallgputasks.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/reportgpuusage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/reportgpuusage.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/resourcedivision.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/resourcedivision.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/taskassignment.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/taskassignment.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/usergpuids.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/usergpuids.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectory/energyframe.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectory/trajectoryframe.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mimic/communicator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mimic/utilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mimic/utilities.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o -c /<<PKGBUILDDIR>>/build/mpich/src/gromacs/utility/baseversion-gen.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/checkpoint.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/confio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/confio.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/enxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/enxio.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.h:39,
from /<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.cpp:37:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void gmx::MimicCommunicator::sendForces(gmx::ArrayRef<gmx::BasicVector<float> >, int)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/espio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/espio.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/filetypes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/filetypes.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/g96io.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/gmx_internal_xdr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmx_internal_xdr.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/gmxfio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/gmxfio_xdr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio_xdr.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.cpp:39:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {}; _Tp = gmx_file_position_t; _Alloc = std::allocator<gmx_file_position_t>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx_file_position_t>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx_file_position_t*, std::vector<gmx_file_position_t> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In function 'std::vector<gmx_file_position_t> gmx_fio_get_output_file_positions()':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx_file_position_t*, std::vector<gmx_file_position_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/groio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/groio.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/libxdrf.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/matio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/md5.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/md5.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/mrcdensitymap.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mrcdensitymap.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/mrcdensitymapheader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mrcdensitymapheader.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/mrcserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mrcserializer.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mtxio.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/oenv.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/pdbio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/pdbio.cpp
/<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp: In function 't_matelmt searchcmap(gmx::ArrayRef<const t_mapping>, t_xpmelmt)':
/<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp:114:11: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
114 | t_matelmt searchcmap(ArrayRef<const t_mapping> map, t_xpmelmt c)
| ^~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/readinp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/readinp.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/timecontrol.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/timecontrol.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/tngio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tngio.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tpxio.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/trrio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/trrio.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/trxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/trxio.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/vmdio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/vmdio.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/warninp.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/writeps.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/xdrd.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/writeps.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/writeps.cpp:39:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_rgb}; _Tp = t_rgb; _Alloc = std::allocator<t_rgb>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_rgb>::iterator' {aka '__gnu_cxx::__normal_iterator<t_rgb*, std::vector<t_rgb> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_rgb>::iterator' {aka '__gnu_cxx::__normal_iterator<t_rgb*, std::vector<t_rgb> >'} changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In function 'gmx::index search_col(t_psdata*, real, real, real)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_rgb*, std::vector<t_rgb> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/xtcio.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/xvgr.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/centerofmass.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/centerofmass.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/compiler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/compiler.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/evaluate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/evaluate.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/indexutil.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/mempool.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/mempool.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/params.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/params.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/parsetree.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/poscalc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/poscalc.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/position.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/position.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/scanner_internal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/scanner_internal.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selection.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selectioncollection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selectioncollection.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selectionoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selectionoption.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selectionoptionbehavior.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selectionoptionbehavior.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selectionoptionmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selectionoptionmanager.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selelem.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selelem.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selhelp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selhelp.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selmethod.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selmethod.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selvalue.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selvalue.cpp
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/usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun.dir/mdrun_main.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../bin/mdrun_mpi.mpich ../../lib/libgromacs_mdrun_mpi.mpich.a /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lpthread -lm /usr/lib/gcc/arm-linux-gnueabihf/9/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so
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cd /<<PKGBUILDDIR>>/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp/CMakeFiles/release-version-info.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/selection /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/selection /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/errhandler.cpp
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/selection && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -std=c++14 -o CMakeFiles/scanner.dir/parser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/parser.cpp
Scanning dependencies of target tng_io_obj
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make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/bwlzh.c
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cd /<<PKGBUILDDIR>>/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color=
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make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -std=c++14 -o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -c /<<PKGBUILDDIR>>/src/external/lmfit/lmmin.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/tmpi_malloc.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/atomic.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/lock.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/pthreads.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/bwt.c
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/system_error.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/system_error.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/coder.c
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
[ 1%] Built target thread_mpi
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/selection && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -std=c++14 -o CMakeFiles/scanner.dir/scanner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/scanner.cpp
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make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/linearalgebra /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/linearalgebra /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake --color=
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make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/linearalgebra && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/eigensolver.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/dict.c
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/fixpoint.c
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/linearalgebra && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/gmx_arpack.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/huffman.c
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/linearalgebra && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/matrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/matrix.cpp
/usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/modularsimulator /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake --color=
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/usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/checkpointhelper.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/huffmem.c
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/lz77.c
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/merge_sort.c
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/mtf.c
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/rle.c
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/tng_compress.c
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/checkpointhelper.cpp: In member function 'void gmx::CheckpointHelper::writeCheckpoint(gmx::Step, gmx::Time)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/checkpointhelper.cpp:129:37: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
129 | mdoutf_write_to_trajectory_files(fplog_, cr_, trajectoryElement_->outf_, MDOF_CPT,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
130 | globalNumAtoms_, step, time, localStateInstance_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
131 | state_global_, observablesHistory_, ArrayRef<RVec>());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/compositesimulatorelement.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/linearalgebra && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/nrjac.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/nrjac.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/linearalgebra && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/sparsematrix.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/vals16.c
[ 2%] Built target linearalgebra
/usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp/src/programs /<<PKGBUILDDIR>>/build/mpich-dp/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun_objlib
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
/usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/programs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/mdrun.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/warnmalloc.c
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/widemuldiv.c
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
[ 2%] Built target scanner
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/xtc2.c
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/constraintelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/constraintelement.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/xtc3.c
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/domdechelper.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/domdechelper.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/energyelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/energyelement.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/programs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/nonbonded_bench.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/lib/tng_io.c
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/forceelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/forceelement.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
[ 2%] Built target mdrun_objlib
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/lib/md5.c
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/forceelement.cpp: In member function 'void gmx::ForceElement::run(gmx::Step, gmx::Time, unsigned int)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/forceelement.cpp:159:13: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
159 | do_force(fplog_, cr_, ms, inputrec_, awh, enforcedRotation_, imdSession_, pull_work_, step,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
160 | nrnb_, wcycle_, localTopology_, box, x, hist, forces, force_vir, mdAtoms_->mdatoms(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
161 | energyElement_->enerdata(), fcd_, lambda, graph, fr_, runScheduleWork_, vsite_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
162 | energyElement_->muTot(), time, ed, static_cast<int>(flags), ddBalanceRegionHandler_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/freeenergyperturbationelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/freeenergyperturbationelement.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/modularsimulator.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/energyelement.cpp: In member function 'void gmx::EnergyElement::doStep(gmx::Time, bool, bool)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/energyelement.cpp:239:17: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
239 | sum_dhdl(enerd_, freeEnergyPerturbationElement_->constLambdaView(), *inputrec_->fepvals);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/parrinellorahmanbarostat.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/freeenergyperturbationelement.cpp: In static member function 'static void std::_Function_handler<void(_ArgTypes ...), _Functor>::_M_invoke(const std::_Any_data&, _ArgTypes&& ...) [with _Functor = gmx::FreeEnergyPerturbationElement::scheduleTask(gmx::Step, gmx::Time, const RegisterRunFunctionPtr&)::<lambda()>; _ArgTypes = {}]':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/freeenergyperturbationelement.cpp:85:27: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
85 | setCurrentLambdasLocal(step, inputrec_->fepvals, lambda0_.data(), lambda_, currentFEPState_);
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/freeenergyperturbationelement.cpp: In constructor 'gmx::FreeEnergyPerturbationElement::FreeEnergyPerturbationElement(FILE*, const t_inputrec*, gmx::MDAtoms*)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/freeenergyperturbationelement.cpp:67:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
67 | initialize_lambdas(fplog_, *inputrec_, true, ¤tFEPState_, lambda_, lambda0_.data());
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/freeenergyperturbationelement.cpp: In member function 'void gmx::FreeEnergyPerturbationElement::updateLambdas(gmx::Step)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/freeenergyperturbationelement.cpp:85:27: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
85 | setCurrentLambdasLocal(step, inputrec_->fepvals, lambda0_.data(), lambda_, currentFEPState_);
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/pmeloadbalancehelper.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/parrinellorahmanbarostat.cpp: In constructor 'gmx::ParrinelloRahmanBarostat::ParrinelloRahmanBarostat(int, int, real, gmx::Step, gmx::ArrayRef<double [3]>, gmx::PropagatorCallbackPtr, gmx::StatePropagatorData*, gmx::EnergyElement*, FILE*, const t_inputrec*, const gmx::MDAtoms*, const t_state*, t_commrec*, bool)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/parrinellorahmanbarostat.cpp:62:1: note: parameter passing for argument of type 'gmx::ArrayRef<double [3]>' changed in GCC 7.1
62 | ParrinelloRahmanBarostat::ParrinelloRahmanBarostat(int nstpcouple,
| ^~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/propagator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/propagator.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/pmeloadbalancehelper.cpp: In member function 'void gmx::PmeLoadBalanceHelper::run(gmx::Step, gmx::Time)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/pmeloadbalancehelper.cpp:107:19: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
107 | pme_loadbal_do(pme_loadbal_, cr_, (isVerbose_ && MASTER(cr_)) ? stderr : nullptr, fplog_,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
108 | mdlog_, *inputrec_, fr_, statePropagatorData_->constBox(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
109 | statePropagatorData_->constPositionsView().paddedArrayRef(), wcycle_, step,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
110 | step - inputrec_->init_step, &bPMETunePrinting_, false);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/shellfcelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/shellfcelement.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/shellfcelement.cpp: In member function 'void gmx::ShellFCElement::run(gmx::Step, gmx::Time, bool, unsigned int)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/shellfcelement.cpp:185:24: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
185 | relax_shell_flexcon(fplog_, cr_, ms, isVerbose_, enforcedRotation_, step, inputrec_, imdSession_,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
186 | pull_work_, isNSStep, static_cast<int>(flags), localTopology_, constr_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
187 | energyElement_->enerdata(), fcd_, statePropagatorData_->localNumAtoms(), x,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
188 | v, box, lambda, hist, forces, force_vir, mdAtoms_->mdatoms(), nrnb_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
189 | wcycle_, graph, shellfc_, fr_, runScheduleWork_, time,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
190 | energyElement_->muTot(), vsite_, ddBalanceRegionHandler_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/signallers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/signallers.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/topologyholder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/topologyholder.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/trajectoryelement.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp: In function 'virtual void gmx::StatePropagatorData::trajectoryWriterTeardown(gmx_mdoutf*)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:464:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
464 | dd_collect_vec(cr_->dd, localStateBackup_.get(), localStateBackup_->x, globalXRef);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:466:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
466 | dd_collect_vec(cr_->dd, localStateBackup_.get(), localStateBackup_->v, globalVRef);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp: In member function 'void gmx::StatePropagatorData::write(gmx_mdoutf_t, gmx::Step, gmx::Time)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:411:37: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
411 | mdoutf_write_to_trajectory_files(fplog_, cr_, outf, static_cast<int>(mdof_flags),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
412 | totalNumAtoms_, currentStep, currentTime,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
413 | localStateBackup_.get(), globalState_, observablesHistory, f_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:44:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:44:
/usr/include/c++/9/bits/stl_vector.h: In member function 'void gmx::StatePropagatorData::setLocalState(std::unique_ptr<t_state>)':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/vrescalethermostat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/vrescalethermostat.cpp
/usr/include/c++/9/bits/stl_vector.h: In function 'void gmx::changePinningPolicy(PinnableVector*, gmx::PinningPolicy) [with PinnableVector = gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >]':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/stophandler.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/isimulator.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/modularsimulator.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/modularsimulator.cpp:44:
/usr/include/c++/9/bits/unique_ptr.h: In member function 'std::unique_ptr<gmx::ISimulatorElement> gmx::ModularSimulator::buildIntegrator(gmx::SignallerBuilder<gmx::NeighborSearchSignaller>*, gmx::SignallerBuilder<gmx::EnergySignaller>*, gmx::SignallerBuilder<gmx::LoggingSignaller>*, gmx::TrajectoryElementBuilder*, std::vector<gmx::ICheckpointHelperClient*>*, gmx::CheckBondedInteractionsCallbackPtr*, gmx::compat::not_null<gmx::StatePropagatorData*>, gmx::compat::not_null<gmx::EnergyElement*>, gmx::FreeEnergyPerturbationElement*, bool)':
/usr/include/c++/9/bits/unique_ptr.h:857:30: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
857 | { return unique_ptr<_Tp>(new _Tp(std::forward<_Args>(__args)...)); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/unique_ptr.h:857:30: note: parameter passing for argument of type 'gmx::ArrayRef<double [3]>' changed in GCC 7.1
857 | { return unique_ptr<_Tp>(new _Tp(std::forward<_Args>(__args)...)); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/unique_ptr.h:857:30: note: parameter passing for argument of type 'gmx::ArrayRef<double [3]>' changed in GCC 7.1
857 | { return unique_ptr<_Tp>(new _Tp(std::forward<_Args>(__args)...)); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/unique_ptr.h:857:30: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
857 | { return unique_ptr<_Tp>(new _Tp(std::forward<_Args>(__args)...)); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In constructor 'gmx::StatePropagatorData::StatePropagatorData(int, FILE*, const t_commrec*, t_state*, int, int, int, int, bool, gmx::FreeEnergyPerturbationElement*, const gmx::TopologyHolder*, bool, bool, std::string, const t_inputrec*, const t_mdatoms*)':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/vrescalethermostat.cpp: In constructor 'gmx::VRescaleThermostat::VRescaleThermostat(int, int, bool, int64_t, int, double, const real*, const real*, const real*, gmx::EnergyElement*, gmx::ArrayRef<double>, gmx::PropagatorCallbackPtr, const t_state*, t_commrec*, bool)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/vrescalethermostat.cpp:59:1: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
59 | VRescaleThermostat::VRescaleThermostat(int nstcouple,
| ^~~~~~~~~~~~~~~~~~
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
[ 5%] Built target modularsimulator
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
[ 8%] Built target tng_io_obj
/usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/<<PKGBUILDDIR>>/build/mpich-dp/VersionInfo.cmake -D VERSION_CMAKEIN=/<<PKGBUILDDIR>>/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI= -D GMX_RELEASE_HASH= -D GMX_SOURCE_HASH= -P /<<PKGBUILDDIR>>/cmake/gmxConfigureVersionInfo.cmake
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color=
Scanning dependencies of target libgromacs
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
/usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/alignedallocator.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/any.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/any.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/basenetwork.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/baseversion.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/binaryinformation.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/compare.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/compare.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/coolstuff.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/cstringutil.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/datafilefinder.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/directoryenumerator.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/errorcodes.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/errorformat.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/exceptions.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/fatalerror.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/fileredirector.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/filestream.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/filestream.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/futil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/futil.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/gmxassert.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/gmxassert.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/gmxomp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/gmxomp.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/ikeyvaluetreeerror.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/ikeyvaluetreeerror.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/init.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/init.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/inmemoryserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/inmemoryserializer.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/int64_to_int.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/int64_to_int.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/keyvaluetree.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/keyvaluetree.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/keyvaluetreemdpwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/keyvaluetreemdpwriter.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/keyvaluetreeserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/keyvaluetreeserializer.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/keyvaluetreetransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/keyvaluetreetransform.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/logger.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/logger.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/loggerbuilder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/loggerbuilder.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/messagestringcollector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/messagestringcollector.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/mpiinplacebuffers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/mpiinplacebuffers.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/niceheader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/niceheader.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/path.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/path.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/physicalnodecommunicator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/physicalnodecommunicator.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/pleasecite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/pleasecite.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/programcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/programcontext.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/smalloc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/smalloc.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/strconvert.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/strconvert.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/strdb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/strdb.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/stringstream.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/stringstream.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/stringutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/sysinfo.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/sysinfo.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/textreader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/textreader.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/textwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/textwriter.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/txtdump.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/atomdata.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_setup.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_system.cpp
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/atomdata.cpp: In function 'void nbnxn_atomdata_add_nbat_fshift_to_fshift(const nbnxn_atomdata_t&, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/atomdata.cpp:1484:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1484 | void nbnxn_atomdata_add_nbat_fshift_to_fshift(const nbnxn_atomdata_t& nbat, gmx::ArrayRef<gmx::RVec> fshift)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_setup.cpp: In function 'void Nbnxm::setupAndRunInstance(const gmx::BenchmarkSystem&, const Nbnxm::KernelBenchOptions&, bool)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_setup.cpp:222:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
222 | nbnxn_put_on_grid(nbv.get(), system.box, 0, lowerCorner, upperCorner, nullptr,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
223 | { 0, int(system.coordinates.size()) }, atomDensity, atomInfo,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
224 | system.coordinates, 0, nullptr);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_setup.cpp:50:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Nbnxm::KernelBenchOptions&}; _Tp = Nbnxm::KernelBenchOptions; _Alloc = std::allocator<Nbnxm::KernelBenchOptions>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<Nbnxm::KernelBenchOptions>::iterator' {aka '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_setup.cpp:50:
/usr/include/c++/9/bits/stl_vector.h: In function 'void Nbnxm::bench(int, const Nbnxm::KernelBenchOptions&)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/gridset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernel_common.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernel_common.cpp
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp: In member function 'void Nbnxm::Grid::fillCell(Nbnxm::GridSetData*, nbnxn_atomdata_t*, int, int, const int*, gmx::ArrayRef<const gmx::BasicVector<double> >, Nbnxm::BoundingBox*)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:859:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
859 | void Grid::fillCell(GridSetData* gridSetData,
| ^~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp: In member function 'void Nbnxm::Grid::sortColumnsCpuGeometry(Nbnxm::GridSetData*, int, const int*, gmx::ArrayRef<const gmx::BasicVector<double> >, nbnxn_atomdata_t*, gmx::Range<int>, gmx::ArrayRef<int>)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:987:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
987 | void Grid::sortColumnsCpuGeometry(GridSetData* gridSetData,
| ^~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp: In member function 'void Nbnxm::Grid::sortColumnsGpuGeometry(Nbnxm::GridSetData*, int, const int*, gmx::ArrayRef<const gmx::BasicVector<double> >, nbnxn_atomdata_t*, gmx::Range<int>, gmx::ArrayRef<int>)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:1050:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1050 | void Grid::sortColumnsGpuGeometry(GridSetData* gridSetData,
| ^~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp: In function '_ZN5Nbnxm7GridSet9putOnGridEPA3_KdiPS1_S4_PKN3gmx15UpdateGroupsCogENS5_5RangeIiEEdNS5_8ArrayRefIKiEENSB_IKNS5_11BasicVectorIdEEEEiPSC_P16nbnxn_atomdata_t._omp_fn.0':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp:216:36: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
216 | Grid::calcColumnIndices(grid.dimensions(), updateGroupsCog, atomRange, x, ddZone, move, thread,
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
217 | nthread, gridSetData_.cells, gridWork_[thread].numAtomsPerColumn);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kerneldispatch.cpp
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp: In member function 'void Nbnxm::GridSet::putOnGrid(const real (*)[3], int, const real*, const real*, const gmx::UpdateGroupsCog*, gmx::Range<int>, real, gmx::ArrayRef<const int>, gmx::ArrayRef<const gmx::BasicVector<double> >, int, const int*, nbnxn_atomdata_t*)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp:136:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
136 | void GridSet::putOnGrid(const matrix box,
| ^~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp:223:24: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
223 | grid.setCellIndices(ddZone, cellOffset, &gridSetData_, gridWork_, atomRange, atomInfo.data(), x,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
224 | numAtomsMoved, nbat);
| ~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp: In function '_ZN5Nbnxm4Grid14setCellIndicesEiiPNS_11GridSetDataEN3gmx8ArrayRefINS_8GridWorkEEENS3_5RangeIiEEPKiNS4_IKNS3_11BasicVectorIdEEEEiP16nbnxn_atomdata_t._omp_fn.0':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:1409:39: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1409 | sortColumnsGpuGeometry(gridSetData, ddZone, atinfo, x, nbat, columnRange,
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1410 | gridWork[thread].sortBuffer);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:1404:39: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1404 | sortColumnsCpuGeometry(gridSetData, ddZone, atinfo, x, nbat, columnRange,
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1405 | gridWork[thread].sortBuffer);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp: In static member function 'static void Nbnxm::Grid::calcColumnIndices(const Nbnxm::Grid::Dimensions&, const gmx::UpdateGroupsCog*, gmx::Range<int>, gmx::ArrayRef<const gmx::BasicVector<double> >, int, const int*, int, int, gmx::ArrayRef<int>, gmx::ArrayRef<int>)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:1172:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1172 | void Grid::calcColumnIndices(const Grid::Dimensions& gridDims,
| ^~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp: In member function 'void Nbnxm::Grid::setCellIndices(int, int, Nbnxm::GridSetData*, gmx::ArrayRef<Nbnxm::GridWork>, gmx::Range<int>, const int*, gmx::ArrayRef<const gmx::BasicVector<double> >, int, nbnxn_atomdata_t*)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:1286:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1286 | void Grid::setCellIndices(int ddZone,
| ^~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/kerneldispatch.cpp: In member function 'void nonbonded_verlet_t::dispatchNonbondedKernel(gmx::InteractionLocality, const interaction_const_t&, const gmx::StepWorkload&, int, const t_forcerec&, gmx_enerdata_t*, t_nrnb*)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/kerneldispatch.cpp:442:33: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
442 | nbnxn_kernel_gpu_ref(
| ~~~~~~~~~~~~~~~~~~~~^
443 | pairlistSet.gpuList(), nbat.get(), &ic, fr.shift_vec, stepWork, clearF,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
444 | nbat->out[0].f, nbat->out[0].fshift.data(), enerd->grpp.ener[egCOULSR].data(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
445 | fr.bBHAM ? enerd->grpp.ener[egBHAMSR].data() : enerd->grpp.ener[egLJSR].data());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_ref.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_ref_prune.cpp
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp: In function 'void nbnxn_kernel_gpu_ref(const NbnxnPairlistGpu*, const nbnxn_atomdata_t*, const interaction_const_t*, real (*)[3], const gmx::StepWorkload&, int, gmx::ArrayRef<double>, real*, real*, real*)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp:57:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
57 | void nbnxn_kernel_gpu_ref(const NbnxnPairlistGpu* nbl,
| ^~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_prune.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_prune.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm_geometry.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm_setup.cpp
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp: In function 'void nbnxn_put_on_grid(nonbonded_verlet_t*, const real (*)[3], int, const real*, const real*, const gmx::UpdateGroupsCog*, gmx::Range<int>, real, gmx::ArrayRef<const int>, gmx::ArrayRef<const gmx::BasicVector<double> >, int, const int*)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:57:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
57 | void nbnxn_put_on_grid(nonbonded_verlet_t* nb_verlet,
| ^~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:53:
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairsearch.h:184:27: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
184 | gridSet_.putOnGrid(box, ddZone, lowerCorner, upperCorner, updateGroupsCog, atomRange,
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
185 | atomDensity, atomInfo, x, numAtomsMoved, move, nbat);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp: In function 'void nbnxn_put_on_grid_nonlocal(nonbonded_verlet_t*, const gmx_domdec_zones_t*, gmx::ArrayRef<const int>, gmx::ArrayRef<const gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:76:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
76 | void nbnxn_put_on_grid_nonlocal(nonbonded_verlet_t* nbv,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:53:
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairsearch.h:184:27: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
184 | gridSet_.putOnGrid(box, ddZone, lowerCorner, upperCorner, updateGroupsCog, atomRange,
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
185 | atomDensity, atomInfo, x, numAtomsMoved, move, nbat);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp: In member function 'void nonbonded_verlet_t::convertCoordinates(gmx::AtomLocality, bool, gmx::ArrayRef<const gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:126:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
126 | void nonbonded_verlet_t::convertCoordinates(const gmx::AtomLocality locality,
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:126:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp: In member function 'void nonbonded_verlet_t::atomdata_add_nbat_f_to_f(gmx::AtomLocality, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:159:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
159 | void nonbonded_verlet_t::atomdata_add_nbat_f_to_f(const gmx::AtomLocality locality,
| ^~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist_tuning.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairlistparams.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlistparams.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairlistset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlistset.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairsearch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairsearch.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/prunekerneldispatch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/prunekerneldispatch.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpcontext.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpmodule.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpwriter.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineinit.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinemodule.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodulemanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinemodulemanager.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlineoptionsmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineoptionsmodule.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist.cpp:38:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::PinningPolicy}; _Tp = NbnxnPairlistGpu; _Alloc = std::allocator<NbnxnPairlistGpu>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<NbnxnPairlistGpu>::iterator' {aka '__gnu_cxx::__normal_iterator<NbnxnPairlistGpu*, std::vector<NbnxnPairlistGpu> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In constructor 'PairlistSet::PairlistSet(gmx::InteractionLocality, const PairlistParams&)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<NbnxnPairlistGpu*, std::vector<NbnxnPairlistGpu> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<NbnxnPairlistGpu*, std::vector<NbnxnPairlistGpu> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineparser.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlineprogramcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineprogramcontext.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/filenm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/pargs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/shellcompletions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/shellcompletions.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/viewit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/viewit.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/atomdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/atomdistribution.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/box.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/cellsizes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/cellsizes.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/collect.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp: In function 'void low_set_ddbox(int, int, const int (*)[3], const real (*)[3], bool, gmx::ArrayRef<const gmx::BasicVector<double> >, const MPI_Comm*, gmx_ddbox_t*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:232:13: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
232 | static void low_set_ddbox(int numPbcDimensions,
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp: In function 'void set_ddbox(const gmx_domdec_t&, bool, const real (*)[3], bool, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx_ddbox_t*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:278:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
278 | void set_ddbox(const gmx_domdec_t& dd,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:291:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
291 | low_set_ddbox(dd.unitCellInfo.npbcdim, dd.unitCellInfo.numBoundedDimensions, &dd.nc, box,
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
292 | calculateUnboundedSize, xRef,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
293 | needToReduceCoordinateData ? &dd.mpi_comm_all : nullptr, ddbox);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:291:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp: In function 'void set_ddbox_cr(const t_commrec&, const int (*)[3], const t_inputrec&, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, gmx_ddbox_t*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:302:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
302 | void set_ddbox_cr(const t_commrec& cr,
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:311:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
311 | low_set_ddbox(ePBC2npbcdim(ir.ePBC), inputrec2nboundeddim(&ir), dd_nc, box, true, x, nullptr, ddbox);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/distribute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp: In function 'void dd_collect_vec(gmx_domdec_t*, const t_state*, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:228:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
228 | void dd_collect_vec(gmx_domdec_t* dd,
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:228:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp: In function 'void dd_collect_state(gmx_domdec_t*, const t_state*, t_state*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:291:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
291 | dd_collect_vec(dd, state_local, state_local->x, globalXRef);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:296:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
296 | dd_collect_vec(dd, state_local, state_local->v, globalVRef);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:301:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
301 | dd_collect_vec(dd, state_local, state_local->cg_p, globalCgpRef);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/dlb.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/dlbtiming.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_constraints.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_network.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp: In function 'void ddSendrecv(const gmx_domdec_t*, int, int, gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:118:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
118 | void ddSendrecv(const gmx_domdec_t* dd,
| ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:118:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:118:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp: In function 'void ddSendrecv(const gmx_domdec_t*, int, int, gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = gmx::BasicVector<double>]':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:118:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:118:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:118:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_setup.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'gmx_bool test_dd_cutoff(t_commrec*, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, real)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3156:17: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3156 | static gmx_bool test_dd_cutoff(t_commrec* cr, const matrix box, gmx::ArrayRef<const gmx::RVec> x, real cutoffRequested)
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3166:14: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3166 | set_ddbox(*dd, false, box, true, x, &ddbox);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'gmx_bool change_dd_cutoff(t_commrec*, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, real)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3228:10: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3228 | gmx_bool change_dd_cutoff(t_commrec* cr, const matrix box, gmx::ArrayRef<const gmx::RVec> x, real cutoffRequested)
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_setup.cpp: In function 'DDGridSetup getDDGridSetup(const gmx::MDLogger&, const t_commrec*, int, const gmx::DomdecOptions&, const DDSettings&, const DDSystemInfo&, real, const gmx_mtop_t&, const t_inputrec&, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, gmx_ddbox_t*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_setup.cpp:906:13: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
906 | DDGridSetup getDDGridSetup(const gmx::MDLogger& mdlog,
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_setup.cpp:934:21: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
934 | set_ddbox_cr(*cr, &numDomainsLegacyIvec, ir, box, xGlobal, ddbox);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_setup.cpp:938:21: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
938 | set_ddbox_cr(*cr, nullptr, ir, box, xGlobal, ddbox);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_specatomcomm.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In constructor 'gmx::DomainDecompositionBuilder::Impl::Impl(const gmx::MDLogger&, t_commrec*, const gmx::DomdecOptions&, const gmx::MdrunOptions&, bool, const gmx_mtop_t&, const t_inputrec&, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3045:1: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3045 | DomainDecompositionBuilder::Impl::Impl(const MDLogger& mdlog,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:2967:82: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2967 | gridSetupCellsizeLimit, mtop, ir, box, xGlobal, &ddbox);
| ^
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3091:92: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3091 | gridSetupCellsizeLimit, mtop_, ir_, box, xGlobal, &ddbox_);
| ^
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_topology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_topology.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In constructor 'gmx::DomainDecompositionBuilder::DomainDecompositionBuilder(const gmx::MDLogger&, t_commrec*, const gmx::DomdecOptions&, const gmx::MdrunOptions&, bool, const gmx_mtop_t&, const t_inputrec&, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3134:1: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3134 | DomainDecompositionBuilder::DomainDecompositionBuilder(const MDLogger& mdlog,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3143:95: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3143 | impl_(new Impl(mdlog, cr, options, mdrunOptions, prefer1DAnd1Pulse, mtop, ir, box, xGlobal))
| ^
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'void dd_atom_spread_real(gmx_domdec_t*, real*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:531:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
531 | ddSendrecv(dd, d, dddirBackward, sendBuffer, receiveBuffer);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:531:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:531:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_vsite.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'void dd_atom_sum_real(gmx_domdec_t*, real*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:595:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
595 | ddSendrecv(dd, d, dddirForward, sendBuffer, receiveBuffer);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:595:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:595:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'void dd_move_x(gmx_domdec_t*, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >, gmx_wallcycle*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:272:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
272 | void dd_move_x(gmx_domdec_t* dd, const matrix box, gmx::ArrayRef<gmx::RVec> x, gmx_wallcycle* wcycle)
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:349:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
349 | ddSendrecv(dd, d, dddirBackward, sendBuffer, receiveBuffer);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:349:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:349:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'void dd_move_f(gmx_domdec_t*, gmx::ForceWithShiftForces*, gmx_wallcycle*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:424:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
424 | ddSendrecv(dd, d, dddirForward, sendBuffer, receiveBuffer);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:424:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:424:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/dump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/dump.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/ga2la.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/ga2la.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/gpuhaloexchange_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/gpuhaloexchange_impl.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/localatomset.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/localatomsetdata.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/localatomsetmanager.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/mdsetup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/mdsetup.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/partition.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/redistribute.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/utility.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/utility.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/domdec/utility.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/domdec/utility.cpp:45:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/domdec/utility.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/domdec/utility.cpp:45:
/usr/include/c++/9/bits/stl_vector.h: In function 'void dd_resize_state(t_state*, PaddedHostVector<gmx::BasicVector<double> >*, int)':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp: In function 'void dd_move_cellx(gmx_domdec_t*, const gmx_ddbox_t*, real*, real*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:253:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
253 | ddSendrecv(dd, d, dddirBackward, gmx::arrayRefFromArray(&buf_s[0].min0, numReals),
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
254 | gmx::arrayRefFromArray(&buf_r[0].min0, numReals));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:253:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:253:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/3dtransforms.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/coordinatetransformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/densityfit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/densityfit.cpp
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function 'void gmx::ScaleCoordinates::Impl::scale(gmx::ArrayRef<gmx::BasicVector<double> >) const':
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:65:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
65 | void ScaleCoordinates::Impl::scale(ArrayRef<RVec> coordinates) const
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function 'void gmx::ScaleCoordinates::Impl::inverseIgnoringZeroScale(gmx::ArrayRef<gmx::BasicVector<double> >) const':
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:75:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
75 | void ScaleCoordinates::Impl::inverseIgnoringZeroScale(ArrayRef<RVec> coordinates) const
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function 'void gmx::ScaleCoordinates::operator()(gmx::ArrayRef<gmx::BasicVector<double> >) const':
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:97:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
97 | void ScaleCoordinates::operator()(ArrayRef<RVec> coordinates) const
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function 'void gmx::ScaleCoordinates::inverseIgnoringZeroScale(gmx::ArrayRef<gmx::BasicVector<double> >) const':
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:102:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
102 | void ScaleCoordinates::inverseIgnoringZeroScale(ArrayRef<RVec> coordinates) const
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function 'void gmx::TranslateAndScale::Impl::transform(gmx::ArrayRef<gmx::BasicVector<double> >) const':
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:140:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
140 | void TranslateAndScale::Impl::transform(ArrayRef<RVec> coordinates) const
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function 'void gmx::TranslateAndScale::operator()(gmx::ArrayRef<gmx::BasicVector<double> >) const':
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:161:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
161 | void TranslateAndScale::operator()(ArrayRef<RVec> coordinates) const
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/densityfittingforce.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/densityfittingforce.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/domdec/partition.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:46:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_range_insert(std::vector<_Tp, _Alloc>::iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/9/bits/vector.tcc:721:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >'} changed in GCC 7.1
721 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:721:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:721:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/domdec/partition.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:46:
/usr/include/c++/9/bits/stl_vector.h: In function 'void setup_dd_communication(gmx_domdec_t*, real (*)[3], gmx_ddbox_t*, t_forcerec*, t_state*, PaddedHostVector<gmx::BasicVector<double> >*)':
/usr/include/c++/9/bits/stl_vector.h:1662:4: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >'} changed in GCC 7.1
1662 | _M_range_insert(__pos, __first, __last,
| ^~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1662:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2104:34: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
2104 | ddSendrecv<gmx::RVec>(dd, dim_ind, dddirBackward, work.positionBuffer, rvecBufferRef);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2104:34: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2104:34: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/do_fit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/do_fit.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/exponentialmovingaverage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/exponentialmovingaverage.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp: In function 'void dd_partition_system(FILE*, const gmx::MDLogger&, int64_t, const t_commrec*, gmx_bool, int, t_state*, const gmx_mtop_t&, const t_inputrec*, gmx::ImdSession*, pull_t*, t_state*, PaddedHostVector<gmx::BasicVector<double> >*, gmx::MDAtoms*, gmx_localtop_t*, t_forcerec*, gmx_vsite_t*, gmx::Constraints*, t_nrnb*, gmx_wallcycle*, gmx_bool)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2866:18: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2866 | set_ddbox(*dd, true, DDMASTER(dd) ? state_global->box : nullptr, true, xGlobal, &ddbox);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2907:18: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2907 | set_ddbox(*dd, bMasterState, state_local->box, true, state_local->x, &ddbox);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2928:18: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2928 | set_ddbox(*dd, bMasterState, state_local->box, bNStGlobalComm, state_local->x, &ddbox);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2946:39: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2946 | comm->updateGroupsCog->addCogs(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
2947 | gmx::arrayRefFromArray(dd->globalAtomGroupIndices.data(), dd->ncg_home), state_local->x);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2946:39: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2970:43: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2970 | comm->updateGroupsCog->addCogs(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
2971 | gmx::arrayRefFromArray(dd->globalAtomGroupIndices.data(), dd->ncg_home),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2972 | state_local->x);
| ~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2970:43: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:3005:26: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3005 | nbnxn_put_on_grid(fr->nbv.get(), state_local->box, 0, comm->zones.size[0].bb_x0,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
3006 | comm->zones.size[0].bb_x1, comm->updateGroupsCog.get(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
3007 | { 0, dd->ncg_home }, comm->zones.dens_zone0, fr->cginfo, state_local->x,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
3008 | ncg_moved, bRedist ? comm->movedBuffer.data() : nullptr);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/functions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/functions.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/gausstransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/gausstransform.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/invertmatrix.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/units.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/units.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/utilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/utilities.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/veccompare.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/veccompare.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/vecdump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/vecdump.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/df_history.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/group.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/iforceprovider.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -Wno-class-memaccess -o CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/inputrec.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/md_enums.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/observableshistory.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpformat.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp: In function 'real (* makeRvecArray(gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::index))[3]':
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:208:7: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
208 | rvec* makeRvecArray(gmx::ArrayRef<const gmx::RVec> v, gmx::index n)
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp: In function 'void initialize_lambdas(FILE*, const t_inputrec&, bool, int*, gmx::ArrayRef<double>, double*)':
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:282:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
282 | void initialize_lambdas(FILE* fplog,
| ^~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:40:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:40:
/usr/include/c++/9/bits/stl_vector.h: In function 'void init_gtc_state(t_state*, int, int, int)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:40:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpmanager.cpp
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:40:
/usr/include/c++/9/bits/stl_vector.h: In function 'void state_change_natoms(t_state*, int)':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helptopic.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpwritercontext.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/rstparser.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/boxutilities.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/mshift.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc_simd.cpp
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp: In function 'void put_atoms_in_box(int, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp:1394:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1394 | void put_atoms_in_box(int ePBC, const matrix box, gmx::ArrayRef<gmx::RVec> x)
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp: In function 'void put_atoms_in_box_omp(int, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >, int)':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp:1454:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1454 | void put_atoms_in_box_omp(int ePBC, const matrix box, gmx::ArrayRef<gmx::RVec> x, gmx_unused int nth)
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp: In function 'void put_atoms_in_triclinic_unitcell(int, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp:1470:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1470 | void put_atoms_in_triclinic_unitcell(int ecenter, const matrix box, gmx::ArrayRef<gmx::RVec> x)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp: In function 'void put_atoms_in_compact_unitcell(int, int, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp:1527:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1527 | void put_atoms_in_compact_unitcell(int ePBC, int ecenter, const matrix box, gmx::ArrayRef<gmx::RVec> x)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp:1527:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcenums.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/rmpbc.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/random/seed.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/seed.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tabulatednormaldistribution.cpp
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp: In function 'void put_molecule_com_in_box(int, int, t_block*, int, t_atom*, int, real (*)[3], real (*)[3])':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp:289:46: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
289 | put_atoms_in_compact_unitcell(ePBC, ecenter, box, newComArrayRef);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp:289:46: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp: In function 'void put_residue_com_in_box(int, int, int, t_atom*, int, real (*)[3], real (*)[3])':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp:341:50: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
341 | put_atoms_in_compact_unitcell(ePBC, ecenter, box, newComArrayRef);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp:341:50: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp:341:50: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp:341:50: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/forcetable.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp: In constructor 'gmx::CubicSplineTable::CubicSplineTable(std::initializer_list<gmx::NumericalSplineTableInput>, const std::pair<double, double>&, real)':
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp:383:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
383 | CubicSplineTable::CubicSplineTable(std::initializer_list<NumericalSplineTableInput> numericalInputList,
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp:383:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp: In constructor 'gmx::QuadraticSplineTable::QuadraticSplineTable(std::initializer_list<gmx::NumericalSplineTableInput>, const std::pair<double, double>&, real)':
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp:367:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
367 | QuadraticSplineTable::QuadraticSplineTable(std::initializer_list<NumericalSplineTableInput> numericalInputList,
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp:170:99: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
170 | std::vector<double> thirdDerivative(internal::vectorSecondDerivative(derivative, inputSpacing));
| ^
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/cyclecounter.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/wallcycle.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/walltime_accounting.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atomprop.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'real gmx::internal::findSmallestQuotientOfFunctionAndSecondDerivative(gmx::ArrayRef<const double>, double, const std::pair<double, double>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:211:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
211 | real findSmallestQuotientOfFunctionAndSecondDerivative(ArrayRef<const double> function,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'real gmx::internal::findSmallestQuotientOfFunctionAndThirdDerivative(gmx::ArrayRef<const double>, double, const std::pair<double, double>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:291:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
291 | real findSmallestQuotientOfFunctionAndThirdDerivative(ArrayRef<const double> function,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'std::vector<double> gmx::internal::vectorSecondDerivative(gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:310:21: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
310 | std::vector<double> vectorSecondDerivative(ArrayRef<const double> f, double spacing)
| ^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'void gmx::internal::throwUnlessDerivativeIsConsistentWithFunction(gmx::ArrayRef<const double>, gmx::ArrayRef<const double>, double, const std::pair<double, double>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:112:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
112 | void throwUnlessDerivativeIsConsistentWithFunction(ArrayRef<const double> function,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:112:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/atoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atoms.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/utility/fatalerror.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/topology/atomprop.cpp:53:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {BaseEntry}; _Tp = BaseEntry; _Alloc = std::allocator<BaseEntry>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<BaseEntry>::iterator' {aka '__gnu_cxx::__normal_iterator<BaseEntry*, std::vector<BaseEntry> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In function 'void readProperty(AtomProperty*, ResidueType*, double)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BaseEntry*, std::vector<BaseEntry> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atomsbuilder.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/block.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/block.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/exclusionblocks.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/forcefieldparameters.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/idef.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/idef.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/ifunc.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/index.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/index.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/invblock.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/invblock.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/mtop_util.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/residuetypes.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/symtab.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/symtab.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/topology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/topology.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/topsort.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/topsort.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/swap/swapcoords.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/essentialdynamics/edsam.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pulling/output.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/output.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/swap/swapcoords.cpp:52:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::LocalAtomSet}; _Tp = swap_group; _Alloc = std::allocator<swap_group>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<swap_group>::iterator' {aka '__gnu_cxx::__normal_iterator<swap_group*, std::vector<swap_group> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In function 't_swap* init_swapcoords(FILE*, const t_inputrec*, const char*, gmx_mtop_t*, const t_state*, ObservablesHistory*, t_commrec*, gmx::LocalAtomSetManager*, const gmx_output_env_t*, const gmx::MdrunOptions&, gmx::StartingBehavior)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<swap_group*, std::vector<swap_group> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pulling/pull.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pulling/pull_rotation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pull_rotation.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/essentialdynamics/edsam.cpp:48:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {edpar&}; _Tp = edpar; _Alloc = std::allocator<edpar>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<edpar>::iterator' {aka '__gnu_cxx::__normal_iterator<edpar*, std::vector<edpar> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<edpar>::iterator' {aka '__gnu_cxx::__normal_iterator<edpar*, std::vector<edpar> >'} changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In function 'std::vector<edpar> {anonymous}::read_edi_file(const char*, int)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<edpar*, std::vector<edpar> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:39:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_pull_group&, gmx::LocalAtomSet, const bool&}; _Tp = pull_group_work_t; _Alloc = std::allocator<pull_group_work_t>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' {aka '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >'} changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_pull_coord&}; _Tp = pull_coord_work_t; _Alloc = std::allocator<pull_coord_work_t>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pull_coord_work_t>::iterator' {aka '__gnu_cxx::__normal_iterator<pull_coord_work_t*, std::vector<pull_coord_work_t> >'} changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In function 'pull_t* init_pull(FILE*, const pull_params_t*, const t_inputrec*, const gmx_mtop_t*, const t_commrec*, gmx::LocalAtomSetManager*, real)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pull_coord_work_t*, std::vector<pull_coord_work_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:39:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2280:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' {aka '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >'} changed in GCC 7.1
2280 | }
| ^
/<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp: In function 'bool pullCheckPbcWithinGroup(const pull_t&, gmx::ArrayRef<const gmx::BasicVector<double> >, const t_pbc&, int, real)':
/<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:949:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
949 | bool pullCheckPbcWithinGroup(const pull_t& pull,
| ^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:949:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/awh.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/awh.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/gmxlib/network.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:45:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/gmxlib/network.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:45:
/usr/include/c++/9/bits/stl_vector.h: In function 'void allocStatePrevStepPullCom(t_state*, const pull_t*)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/bias.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/biasparams.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biasparams.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.cpp:47:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, const double&, const double&}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >'} changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp: In member function 'void gmx::Bias::updateForceCorrelationGrid(gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:386:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
386 | void Bias::updateForceCorrelationGrid(gmx::ArrayRef<const double> probWeightNeighbor, double t)
| ^~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:406:45: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
406 | state_.calcUmbrellaForceAndPotential(dimParams_, grid_, indexNeighbor, forceFromNeighbor);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:70:
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationgrid.h:104:37: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
104 | tensors_[pointIndex].addData(weight, data, blockLengthMeasure == BlockLengthMeasure::Weight, t);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/biasparams.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/awh/biasparams.cpp:47:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp: In member function 'gmx::ArrayRef<const double> gmx::Bias::calcForceAndUpdateBias(const double*, double*, double*, const t_commrec*, const gmx_multisim_t*, double, int64_t, int64_t, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:144:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
144 | updateForceCorrelationGrid(probWeightNeighbor, t);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
162 | state_.calcConvolvedForce(dimParams_, grid_, probWeightNeighbor, tempForce_, biasForce_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:172:57: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
172 | potential = state_.calcUmbrellaForceAndPotential(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
173 | dimParams_, grid_, coordState.umbrellaGridpoint(), biasForce_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
182 | double newPotential = state_.moveUmbrella(dimParams_, grid_, probWeightNeighbor,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
183 | biasForce_, step, seed, params_.biasIndex);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In constructor 'gmx::BiasParams::BiasParams(const gmx::AwhParams&, const gmx::AwhBiasParams&, const std::vector<gmx::DimParams>&, double, double, gmx::BiasParams::DisableUpdateSkips, int, const std::vector<gmx::GridAxis>&, int)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/biassharing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biassharing.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/biasstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::Bias, std::vector<int, std::allocator<int> >&}; _Tp = gmx::BiasCoupledToSystem; _Alloc = std::allocator<gmx::BiasCoupledToSystem>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BiasCoupledToSystem>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BiasCoupledToSystem*, std::vector<gmx::BiasCoupledToSystem> >'} changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In constructor 'gmx::Awh::Awh(FILE*, const t_inputrec&, const t_commrec*, const gmx_multisim_t*, const gmx::AwhParams&, const string&, pull_t*)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BiasCoupledToSystem*, std::vector<gmx::BiasCoupledToSystem> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/biaswriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biaswriter.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/coordstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/coordstate.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In function 'void gmx::{anonymous}::updateTargetDistribution(gmx::ArrayRef<gmx::PointState>, const gmx::BiasParams&)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:292:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::PointState>' changed in GCC 7.1
292 | void updateTargetDistribution(gmx::ArrayRef<PointState> pointState, const BiasParams& params)
| ^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'double gmx::BiasState::calcUmbrellaForceAndPotential(const std::vector<gmx::DimParams>&, const gmx::Grid&, int, gmx::ArrayRef<double>) const':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:416:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
416 | double BiasState::calcUmbrellaForceAndPotential(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::calcConvolvedForce(const std::vector<gmx::DimParams>&, const gmx::Grid&, gmx::ArrayRef<const double>, gmx::ArrayRef<double>, gmx::ArrayRef<double>) const':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:437:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
437 | void BiasState::calcConvolvedForce(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:437:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:437:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'double gmx::BiasState::moveUmbrella(const std::vector<gmx::DimParams>&, const gmx::Grid&, gmx::ArrayRef<const double>, gmx::ArrayRef<double>, int64_t, int64_t, int)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:467:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
467 | double BiasState::moveUmbrella(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:467:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:476:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
476 | coordState_.sampleUmbrellaGridpoint(grid, coordState_.gridpointIndex(), probWeightNeighbor,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
477 | step, seed, indexSeed);
| ~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:476:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::sampleProbabilityWeights(const gmx::Grid&, gmx::ArrayRef<const double>)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1233:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1233 | void BiasState::sampleProbabilityWeights(const Grid& grid, gmx::ArrayRef<const double> probWeightNeighbor)
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::sampleCoordAndPmf(const gmx::Grid&, gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1287:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1287 | void BiasState::sampleCoordAndPmf(const Grid& grid, gmx::ArrayRef<const double> probWeightNeighbor, double convolvedBias)
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/coordstate.cpp: In member function 'void gmx::CoordState::sampleUmbrellaGridpoint(const gmx::Grid&, int, gmx::ArrayRef<const double>, int64_t, int64_t, int)':
/<<PKGBUILDDIR>>/src/gromacs/awh/coordstate.cpp:129:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
129 | void CoordState::sampleUmbrellaGridpoint(const Grid& grid,
| ^~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/correlationgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/correlationgrid.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/correlationhistory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/correlationhistory.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::updateFreeEnergyAndAddSamplesToHistogram(const std::vector<gmx::DimParams>&, const gmx::Grid&, const gmx::BiasParams&, const t_commrec*, const gmx_multisim_t*, double, int64_t, FILE*, std::vector<int>*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
1072 | double newHistogramSize = histogramSize_.newHistogramSize(params, t, detectedCovering, points_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1073 | weightSumCovering_, fplog);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/correlationtensor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/grid.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/histogramsize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp: In member function 'void gmx::CorrelationTensor::addData(double, gmx::ArrayRef<const double>, bool, double)':
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp:229:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
229 | void CorrelationTensor::addData(double weight, gmx::ArrayRef<const double> data, bool blockLengthInWeight, double t)
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp:229:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp: In member function 'double gmx::HistogramSize::newHistogramSizeInitialStage(const gmx::BiasParams&, double, bool, gmx::ArrayRef<double>, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp:77:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
77 | double HistogramSize::newHistogramSizeInitialStage(const BiasParams& params,
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp: In member function 'double gmx::HistogramSize::newHistogramSize(const gmx::BiasParams&, double, bool, const std::vector<gmx::PointState>&, gmx::ArrayRef<double>, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp:209:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
209 | double HistogramSize::newHistogramSize(const BiasParams& params,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp:47:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {int&, double}; _Tp = gmx::CorrelationBlockData; _Alloc = std::allocator<gmx::CorrelationBlockData>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::CorrelationBlockData>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::CorrelationBlockData*, std::vector<gmx::CorrelationBlockData> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/pointstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/pointstate.cpp
/usr/include/c++/9/bits/vector.tcc: In constructor 'gmx::CorrelationTensor::CorrelationTensor(int, int, double)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::CorrelationBlockData*, std::vector<gmx::CorrelationBlockData> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/read_params.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/read_params.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/simd/support.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/support.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/dimparams.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/awh/grid.h:60,
from /<<PKGBUILDDIR>>/src/gromacs/awh/grid.cpp:47:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, double&, double&, double&}; _Tp = gmx::GridAxis; _Alloc = std::allocator<gmx::GridAxis>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::GridAxis>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In constructor 'gmx::Grid::Grid(const std::vector<gmx::DimParams>&, const gmx::AwhDimParams*)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&, const double&, double, int&}; _Tp = gmx::GridAxis; _Alloc = std::allocator<gmx::GridAxis>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::GridAxis>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In function 'void gmx::mapGridToDataGrid(std::vector<int>*, const double* const*, int, const string&, const gmx::Grid&, const string&)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/imd/imd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/imd/imd.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/imd/imdsocket.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxlib/conformation_utilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/conformation_utilities.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxlib/network.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/network.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxlib/nrnb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nrnb.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_free_energy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_free_energy.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/boxdeformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/boxdeformation.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/broadcaststructs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/boxdeformation.cpp: In member function 'void gmx::BoxDeformation::apply(gmx::ArrayRef<gmx::BasicVector<double> >, real (*)[3], int64_t)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/boxdeformation.cpp:106:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
106 | void BoxDeformation::apply(ArrayRef<RVec> x, matrix box, int64_t step)
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.cpp:40:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/calc_verletbuf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/calc_verletbuf.cpp
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.cpp:40:
/usr/include/c++/9/bits/stl_vector.h: In function 'void broadcastStateWithoutDynamics(const t_commrec*, t_state*)':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/calcmu.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/calcmu.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/calcmu.cpp: In function 'void calc_mu(int, int, gmx::ArrayRef<gmx::BasicVector<double> >, const real*, const real*, int, double*, double*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/calcmu.cpp:50:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
50 | void calc_mu(int start,
| ^~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/calcvir.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/calcvir.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/calc_verletbuf.h:39,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/calc_verletbuf.cpp:38:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {VerletbufAtomtype}; _Tp = VerletbufAtomtype; _Alloc = std::allocator<VerletbufAtomtype>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<VerletbufAtomtype>::iterator' {aka '__gnu_cxx::__normal_iterator<VerletbufAtomtype*, std::vector<VerletbufAtomtype> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In function 'std::vector<VerletbufAtomtype> getVerletBufferAtomtypes(const gmx_mtop_t&, bool)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<VerletbufAtomtype*, std::vector<VerletbufAtomtype> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/checkpointhandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/checkpointhandler.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/compute_io.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/compute_io.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/constr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/constraintrange.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp: In function 'void gmx::constr_recur(const t_blocka*, const InteractionLists&, gmx::ArrayRef<const t_iparams>, gmx_bool, int, int, int, int*, real, real, real*, int*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp:60:13: note: parameter passing for argument of type 'gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
60 | static void constr_recur(const t_blocka* at2con,
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp: In function 'void gmx::constr_recur(const t_blocka*, const InteractionLists&, gmx::ArrayRef<const t_iparams>, gmx_bool, int, int, int, int*, real, real, real*, int*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp:60:13: note: parameter passing for argument of type 'gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/coupling.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp: In function 't_blocka gmx::make_at2con(const gmx_moltype_t&, gmx::ArrayRef<const t_iparams>, gmx::FlexibleConstraintTreatment)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp:826:10: note: parameter passing for argument of type 'gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
826 | t_blocka make_at2con(const gmx_moltype_t& moltype,
| ^~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/dispersioncorrection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp: In constructor 'DispersionCorrection::TopologyParams::TopologyParams(const gmx_mtop_t&, const t_inputrec&, bool, int, gmx::ArrayRef<const double>)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp:107:1: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
107 | DispersionCorrection::TopologyParams::TopologyParams(const gmx_mtop_t& mtop,
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp: In constructor 'DispersionCorrection::DispersionCorrection(const gmx_mtop_t&, const t_inputrec&, bool, int, gmx::ArrayRef<const double>, const interaction_const_t&, const char*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp:520:1: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
520 | DispersionCorrection::DispersionCorrection(const gmx_mtop_t& mtop,
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp:530:85: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
530 | topParams_(mtop, inputrec, useBuckingham, numAtomTypes, nonbondedForceParameters)
| ^
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/ebin.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp: In function 'void andersen_tcoupl(const t_inputrec*, int64_t, const t_commrec*, const t_mdatoms*, gmx::ArrayRef<gmx::BasicVector<double> >, real, const std::vector<bool>&, gmx::ArrayRef<const double>)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp:810:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
810 | void andersen_tcoupl(const t_inputrec* ir,
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp:810:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/ebin.cpp: In function 'void add_ebin_indexed(t_ebin*, int, gmx::ArrayRef<bool>, gmx::ArrayRef<const double>, gmx_bool)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/ebin.cpp:197:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
197 | void add_ebin_indexed(t_ebin* eb,
| ^~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/enerdata_utils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/energyoutput.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/energyoutput.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp: In function 'void sum_dhdl(gmx_enerdata_t*, gmx::ArrayRef<const double>, const t_lambda&)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp:92:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
92 | void sum_dhdl(gmx_enerdata_t* enerd, gmx::ArrayRef<const real> lambda, const t_lambda& fepvals)
| ^~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/expanded.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/force.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp: In function 'void do_force_lowlevel(t_forcerec*, const t_inputrec*, const t_idef*, const t_commrec*, const gmx_multisim_t*, t_nrnb*, gmx_wallcycle_t, const t_mdatoms*, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, history_t*, gmx::ForceOutputs*, gmx_enerdata_t*, t_fcdata*, const real (*)[3], const real*, const t_graph*, const real (*)[3], const gmx::StepWorkload&, const DDBalanceRegionHandler&)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp:290:40: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
290 | status = gmx_pme_do(
| ~~~~~~~~~~^
291 | fr->pmedata,
| ~~~~~~~~~~~~
292 | gmx::constArrayRefFromArray(coordinates.unpaddedConstArrayRef().data(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
293 | md->homenr - fr->n_tpi),
| ~~~~~~~~~~~~~~~~~~~~~~~~
294 | forceWithVirial.force_, md->chargeA, md->chargeB, md->sqrt_c6A,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
295 | md->sqrt_c6B, md->sigmaA, md->sigmaB, box, cr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
296 | DOMAINDECOMP(cr) ? dd_pme_maxshift_x(cr->dd) : 0,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
297 | DOMAINDECOMP(cr) ? dd_pme_maxshift_y(cr->dd) : 0, nrnb, wcycle,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
298 | ewaldOutput.vir_q, ewaldOutput.vir_lj, &Vlr_q, &Vlr_lj,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
299 | lambda[efptCOUL], lambda[efptVDW], &ewaldOutput.dvdl[efptCOUL],
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
300 | &ewaldOutput.dvdl[efptVDW], pme_flags);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp:290:40: note: parameter passing for argument of type 'const gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp:290:40: note: parameter passing for argument of type 'const gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp:325:40: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
325 | gmx_pme_calc_energy(
| ~~~~~~~~~~~~~~~~~~~^
326 | fr->pmedata,
| ~~~~~~~~~~~~
327 | coordinates.unpaddedConstArrayRef().subArray(md->homenr - fr->n_tpi, fr->n_tpi),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
328 | gmx::arrayRefFromArray(md->chargeA + md->homenr - fr->n_tpi, fr->n_tpi),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
329 | &Vlr_q);
| ~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp:325:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp:325:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/forcerec.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/energyoutput.cpp: In member function 'void gmx::EnergyOutput::addDataAtEnergyStep(bool, bool, double, real, const gmx_enerdata_t*, const t_state*, const t_lambda*, const t_expanded*, const real (*)[3], const real (*)[3], const real (*)[3], const real (*)[3], const real (*)[3], const gmx_ekindata_t*, const real*, const gmx::Constraints*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/energyoutput.cpp:881:21: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
881 | add_ebin_indexed(ebin_, ie_, gmx::ArrayRef<bool>(bEner_), enerd->term, bSum);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/gmx_omp_nthreads.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/forcerec.cpp: In function 'void __static_initialization_and_destruction_0(int, int)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/forcerec.cpp:103:16: warning: ignoring return value of 'char* getenv(const char*)', declared with attribute warn_unused_result [-Wunused-result]
103 | (getenv("GMX_GPU_PME_PP_COMMS") != nullptr) && GMX_THREAD_MPI && (GMX_GPU == GMX_GPU_CUDA);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/groupcoord.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp
In file included from /usr/include/c++/9/memory:80,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.h:40,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/forcerec.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/forcerec.cpp:39:
/usr/include/c++/9/bits/unique_ptr.h: In function 'void init_forcerec(FILE*, const gmx::MDLogger&, t_forcerec*, t_fcdata*, const t_inputrec*, const gmx_mtop_t*, const t_commrec*, real (*)[3], const char*, const char*, gmx::ArrayRef<const std::__cxx11::basic_string<char> >, const gmx_hw_info_t&, const gmx_device_info_t*, bool, bool, real, gmx_wallcycle*)':
/usr/include/c++/9/bits/unique_ptr.h:857:30: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
857 | { return unique_ptr<_Tp>(new _Tp(std::forward<_Args>(__args)...)); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/md_support.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/md_support.cpp: In function 'void setCurrentLambdasLocal(int64_t, const t_lambda*, const double*, gmx::ArrayRef<double>, int)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/md_support.cpp:356:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
356 | void setCurrentLambdasLocal(const int64_t step,
| ^~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.cpp:39:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::HostAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdebin_bar.cpp
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.cpp:39:
/usr/include/c++/9/bits/stl_vector.h: In function 'void atoms2md(const gmx_mtop_t*, const t_inputrec*, int, const int*, int, gmx::MDAtoms*)':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'void gmx::MDAtoms::resize(int)':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In function 'void gmx::changePinningPolicy(PinnableVector*, gmx::PinningPolicy) [with PinnableVector = gmx::PaddedVector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> >]':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp
In file included from /usr/include/c++/9/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:46:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:46:
/usr/include/c++/9/bits/stl_vector.h: In function 'void gmx::set_lincs(const t_idef&, const t_mdatoms&, bool, const t_commrec*, gmx::Lincs*)':
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1335 | _M_fill_insert(begin() + __offset, __n, __x);
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/membed.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp: In function 'void mdoutf_write_to_trajectory_files(FILE*, const t_commrec*, gmx_mdoutf_t, int, int, int64_t, double, t_state*, t_state*, ObservablesHistory*, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp:257:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
257 | void mdoutf_write_to_trajectory_files(FILE* fplog,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp:282:31: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
282 | dd_collect_vec(cr->dd, state_local, state_local->x, globalXRef);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp:287:31: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
287 | dd_collect_vec(cr->dd, state_local, state_local->v, globalVRef);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp:293:27: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
293 | dd_collect_vec(cr->dd, state_local, f_local,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
294 | gmx::arrayRefFromArray(reinterpret_cast<gmx::RVec*>(f_global), f_local.size()));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/nsgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nsgrid.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/perf_est.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qm_gamess.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_gamess.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qm_gaussian.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_gaussian.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qm_mopac.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_mopac.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qm_orca.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_orca.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qmmm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qmmm.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/resethandler.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp: In function 'int add_binr(t_bin*, gmx::ArrayRef<const double>)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp:103:5: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
103 | int add_binr(t_bin* b, gmx::ArrayRef<const real> r)
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp:103:5: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/rf_util.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp: In function 'void extract_binr(t_bin*, int, gmx::ArrayRef<double>)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp:160:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
160 | void extract_binr(t_bin* b, int index, gmx::ArrayRef<real> r)
| ^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/settle.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/sighandler.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/simulationsignal.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/splitter.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/stat.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp: In function 'void do_force(FILE*, const t_commrec*, const gmx_multisim_t*, const t_inputrec*, gmx::Awh*, gmx_enfrot*, gmx::ImdSession*, pull_t*, int64_t, t_nrnb*, gmx_wallcycle_t, const gmx_localtop_t*, const real (*)[3], gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, history_t*, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, real (*)[3], const t_mdatoms*, gmx_enerdata_t*, t_fcdata*, gmx::ArrayRef<double>, t_graph*, t_forcerec*, gmx::MdrunScheduleWorkload*, const gmx_vsite_t*, real*, double, gmx_edsam*, int, const DDBalanceRegionHandler&)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:895:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
895 | void do_force(FILE* fplog,
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1070:43: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1070 | stateGpu->copyCoordinatesToGpu(x.unpaddedArrayRef(), AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1103:41: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1103 | stateGpu->copyCoordinatesFromGpu(x.unpaddedArrayRef(), AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1154:30: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1154 | nbnxn_put_on_grid(nbv, box, 0, vzero, box_diag, nullptr, { 0, mdatoms->homenr }, -1,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1155 | fr->cginfo, x.unpaddedArrayRef(), 0, nullptr);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1161:39: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1161 | nbnxn_put_on_grid_nonlocal(nbv, domdec_zones(cr->dd), fr->cginfo, x.unpaddedArrayRef());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1243:36: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1243 | nbv->convertCoordinates(AtomLocality::Local, false, x.unpaddedArrayRef());
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1243:36: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1320:53: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1320 | stateGpu->copyCoordinatesFromGpu(x.unpaddedArrayRef(), AtomLocality::NonLocal);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1337:51: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1337 | stateGpu->copyCoordinatesToGpu(x.unpaddedArrayRef(), AtomLocality::NonLocal);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1345:40: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1345 | nbv->convertCoordinates(AtomLocality::NonLocal, false, x.unpaddedArrayRef());
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1345:40: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1525:53: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1525 | nbnxn_atomdata_add_nbat_fshift_to_fshift(*nbv->nbat,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
1526 | forceOut.forceWithShiftForces().shiftForces());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1589:46: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1589 | stateGpu->